Jack Henry & Associates (JKHY) 10-K risk factor changes: FY2013 vs FY2012

If the economic environment [removed: remains poor, it may result in significant decreases] [added: worsens, we could face a reduction] in demand [removed: by] [added: from] current and potential clients for our products and services, which could have a material adverse effect on our business, results of operations and financial condition.

The Company could also experience the loss of customers due to their [added: acquisition or] financial failure.

Failures associated with payment transactions could result in [removed: a] financial loss.

[added: The volume and dollar amount] of payment transactions that we process is very large and continues to grow.

If the continuity of operations, integrity of processing, or ability to detect or prevent fraudulent payments were compromised in connection with payments transactions, this could result in [removed: a] financial as well as reputational loss to us.

[removed: If we are unable to obtain such ACH services] in the future, that could have a material adverse effect on our business, financial position and results of operations.

Our primary market consists of approximately [removed: 7,300] [added: 7,000] commercial and savings banks and [removed: 7,300] [added: 7,100] credit unions.

The services we provide to our customers are subject to government regulation that could hinder the development of [removed: portions of] our [removed: business] [added: business, increase costs,] or impose constraints on the way we conduct our operations.

In addition, existing laws, regulations, and policies could be amended or interpreted differently by regulators in a manner that [added: imposes additional costs and] has a negative impact on our existing operations or that limits our future growth or expansion.

[removed: An operational] [added: Operational] failure in our outsourcing facilities could [added: expose us to damage claims, increase regulatory scrutiny and] cause us to lose customers.

Damage or destruction that interrupts our outsourcing operations could [removed: damage] [added: cause delays and failures in customer processing which could hurt] our relationship with [removed: customers] [added: customers, expose us to damage claims,] and [removed: may] cause us to incur substantial additional expense to [added: relocate operations and] repair or replace damaged equipment.

In the event that an interruption [removed: of our network] extends for more than several hours, we may experience data loss or a reduction in revenues by reason of such interruption.

[removed: In addition, a] [added: A] significant interruption of service could have a negative impact on our [removed: reputation and could] [added: reputation, result in damage claims,] lead our present and potential customers to choose other service [removed: providers.][added: providers, and lead to increased regulatory scrutiny of the critical services we provide to financial institutions, with resulting increases in compliance burdens and costs.]

Substantial recent merger and acquisition activity in our industry has affected the availability and pricing of such [added: acquisitions.]

We have acquired a number of businesses in the last [removed: several years] [added: decade] and will continue to explore acquisitions in the future.

If others claim that we have infringed their intellectual property rights, we could be liable for significant [removed: damages.][added: damages or could be required to change our processes.]

In addition, a growing portion of our revenue is derived from transaction processing fees, which depend heavily on levels of consumer and business spending.

Deterioration in general economic conditions could reduce transaction volumes and the Company's related revenues.

If we are unable to obtain such ACH services

The Dodd-Frank Wall Street Reform and Consumer Protection Act, signed into law in 2010, significantly changed the regulation of the financial services industry, producing new regulatory agencies and voluminous new regulations, many of which are still being written.

These new regulations may require additional programming or other costly changes in our processes or personnel.

Our failure to comply with regulations or to meet regulatory expectations could adversely affect our business and results of operations.

While much of our operations are not directly subject to regulations applicable to financial institutions, as a provider of processing services to such institutions, we are examined on a regular basis by various regulatory authorities.

If we fail to comply with applicable regulations or guidelines, we could be subject to regulatory actions or rating changes and suffer harm to our customer relationships and reputation.

Such failures could require significant expenditures to correct and could negatively affect our ability to retain customers and obtain new customers.

If our defense of such claims is not successful,

we could be forced to pay damages or could be subject to injunctions that would cause us to cease making or selling certain applications or force us to redesign applications.

Given this concentration, we may be particularly exposed to the current difficult and unsettled economic climate.

The volume and dollar amount

acquisitions.

Jack Henry & Associates, Inc. (JHA) is headquartered in Monett, Missouri, employs approximately [removed: 4,900] [added: 5,200] associates nationwide, and is a leading provider of technology solutions and payment processing services primarily for financial services organizations.

Its solutions serve more than [removed: 11,900] [added: 11,300] customers and are marketed and supported through three primary brands.

Through internal product development, disciplined acquisitions, and alliances with companies offering niche solutions that complement our proprietary solutions, we regularly introduce new products and services and generate new cross-sales opportunities across our three [removed: marketed] [added: business] brands.

Our support infrastructure and strict standards provide service levels we believe to be the highest in the markets we serve and generate high levels of customer satisfaction and [added: retention.]

The majority of our revenue is derived from recurring outsourcing [removed: fees,] [added: fees and] transaction processing [removed: fees, and support and service] fees that [removed: generally] [added: predominantly] have contract terms of five years or greater.

During the last five fiscal years, our revenues have grown from [removed: $742,926] [added: $745,593] in fiscal [removed: 2008] [added: 2009] to [removed: $1,027,109] [added: $1,129,386] in fiscal [removed: 2012.][added: 2013.]

We are [added: currently] cautiously optimistic regarding ongoing economic improvement and expect [added: our clients] to continue investing in [removed: the] [added: our] products and services [removed: our clients need] [added: that are needed] to improve their operating efficiencies and performance.

We anticipate consolidation within the financial services industry to continue, including [added: some reduced amount of] bank failures and [removed: increased] [added: an increasing amount of] merger and acquisition activity.

Regulatory conditions and legislation such as the Dodd-Frank Wall Street Reform [removed: Act] and Consumer Protection Act will continue to impact the financial services industry and potentially motivate some financial institutions to postpone discretionary spending.

All dollar amounts are in thousands and discussions compare fiscal [removed: 2012] [added: 2013] to fiscal [removed: 2011] [added: 2012] and compare fiscal [removed: 2011] [added: 2012] to fiscal [removed: 2010.][added: 2011.]

Significant portions of our business continue to come from recurring [removed: revenue,] [added: revenue] and [removed: increases in backlog coupled with a] [added: our] healthy sales pipeline [removed: are] [added: is] also encouraging.

| License Revenue | Year Ended | | | | | | | | % | [removed: |]

| License | $ | 54,811 | | | $ | 53,067 | | | [removed: 3] [added: 2] | % |

| Percentage of total revenue | 5 | | % | | [removed: 6] [added: 5] | | % | | | [removed: |]

| Percentage of total revenue | [removed: 1] [added: 90] | | % | | [removed: 1] [added: 89] | | % | | | |

| Gross Profit Margin | [removed: 39] [added: 91] | | % | | [removed: 39] [added: 89] | | % | | | |

| Percentage of total revenue | [removed: 59] [added: <1%] | | [removed: %] | | [removed: 59] [added: 1] | | % | | | |

| Gross Profit Margin | 41 | | % | | [removed: 41] [added: 39] | | % | | | |

Typically, we upgrade our various core and complementary software applications once [removed: per year.]

The decrease in the effective tax rate was primarily due to the completion of the Internal Revenue Service audit of the tax returns for the fiscal years June 30, 2008 and 2009, partially offset by the Research and Experimentation Tax Credit not being extended, effective December 31, [added: 2011.]

We license our proprietary software products under standard license agreements that typically provide the customer with a non-exclusive, non-transferable right to use the software on a single computer and for a single financial [removed: institution location.][added: institution.]

[removed: In addition,] [added: While license fees will fluctuate, recent trends indicate that] our customers are increasingly electing to contract for our products via outsourced delivery rather than a traditional license [added: as our outsourced delivery does not require an up-front capital investment in license fees.]

| Percentage of total revenue | [removed: 88] [added: 53] | | % | | [removed: 86] [added: 54] | | % | | | |

| In-House Support & Other Services | $ | [removed: 16,286] [added: 12,677] | | | [removed: 6] [added: 4] | % | | |

| Electronic Payment Services | [removed: 93,870] [added: 58,052] | | | | [removed: 43] [added: 17] | % | | |

| Outsourcing Services | [removed: 15,574] [added: 23,017] | | | | [removed: 10] [added: 12] | % | | |

| Implementation Services | [removed: 6,019] [added: 12,289] | | | | [removed: 9] [added: 17] | % | | |

Support and service revenues are generated from [removed: implementation services (including conversion, installation, configuration and training),] annual support to assist the customer in operating their systems and to enhance and update the software, [added: electronic payment services,] outsourced data processing services and [removed: electronic payment services.][added: implementation services (including conversion, installation, configuration and training).]

There was [removed: strong] growth in all [added: components of] support and service revenue [removed: components] in fiscal [removed: 2011.][added: 2013.]

[removed: Additionally, annual maintenance fees have increased as our customers’ assets have grown and revenue] [added: Revenue] from our complementary products has [added: also] grown as the total number of supported in-house [removed: customers] [added: products] has grown.

Electronic payment services [removed: continued] [added: continue] to experience the largest [removed: percentage revenue] growth.

Outsourcing services for banks and credit unions continue to drive revenue growth as customers continue to [removed: choose outsourcing] [added: show a preference] for [removed: the] [added: outsourced] delivery of our solutions.

| Percentage of total revenue | [removed: 6] [added: 4] | | % | | [removed: 8] [added: 4] | | % | | | |

Hardware revenue decreased [removed: slightly] due to a decrease in the number of [added: third party] hardware systems and components [removed: delivered compared to last year.][added: delivered.]

Cost of license represents the cost of software from third party vendors through remarketing agreements associated [added: with license fee revenue.]

| License Gross Profit | $ | [removed: 46,782] [added: 49,994] | | | $ | [removed: 46,398] [added: 48,700] | | | [removed: 1] [added: 3] | % |

| Gross Profit Margin | [removed: 88] [added: 26] | | % | | [removed: 89] [added: 27] | | % | | | |

| Percentage of total revenue | [removed: 53] [added: 58] | | % | | [removed: 52] [added: 59] | | % | | | |

| Support and Service Gross Profit | $ | [removed: 336,336] [added: 411,291] | | | $ | [removed: 282,028] [added: 357,891] | | | [removed: 19] [added: 15] | % |

| Hardware Gross Profit | $ | [removed: 16,216] [added: 15,707] | | | $ | [removed: 16,694] [added: 17,139] | | | [removed: (3] [added: (8] | )% |

Support and service fees also include in-house maintenance fees on primarily annual contract terms.

Income from continuing operations has grown from $103,102 in fiscal 2009 to $176,645 in fiscal 2013.

We continue to focus on areas of our company to accomplish our ongoing objective of providing the best integrated solutions, products and customer service available to our clients.

FISCAL 2013 COMPARED TO FISCAL 2012

In fiscal 2013, revenues increased 10% or $102,277 compared to the prior year due primarily to strong growth in all components of support and service revenues, particularly our electronic payment services and our outsourcing services.

The growth in revenue and the Company's continued focus on cost management continued to drive up gross margins, which has resulted in a 13% increase in gross profit.

Operating expenses increased 13% for the year mainly due to expenses related to the impact of widespread flooding caused by Hurricane Sandy on our Lyndhurst, New Jersey item processing center.

Expenses related to this event totaled $12,475 for fiscal 2013, net of $2,390 insurance recoveries received in the year.

Insurance claims have been made by JHA to recover the portions of the remaining expenses incurred related to Hurricane Sandy.

These open insurance recovery claims have not been finalized and no amounts have been recorded in the financial results for the year ended June 30, 2013.

The amount recovered will likely be less than the amount of the expense.

Increased revenue and gross margins, partially offset by increased operating expenses, resulted in a combined 14% increase in net income for fiscal 2013.

We move into fiscal 2014 following record revenue achieved in fiscal 2013.

| | | | | | | | | | |

| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |

| | | | | | | | | | |

| | June 30, | | | | | | | | Change |

| | 2013 | | | | 2012 | | | | |

| License | $ | 54,818 | | | $ | 54,811 | | | <1% |

License revenue has remained consistent to last year due to strong results from our core and complementary Credit Union products being offset by reduced revenue from our Alogent® products (our suite of deposit and image capture products targeted at large financial institutions) which reduced from a particularly strong prior year.

| | 2013 | | | | 2012 | | | | | |

| Support and service | $ | 1,015,211 | | | $ | 909,176 | | | 12 | % |

| Total Increase | $ | 106,035 | | | | | | |

In-house support and other services revenue increased due to annual maintenance fee increases as our customers’ assets grow.

The revenue increases are attributable to strong performance across debit/credit card processing services, online bill payment services and ACH processing.

Implementation services revenue increased due mainly to increased implementations of our core Banking and Credit Union platform products and related complementary products, coupled with higher merger conversion revenues from our core banking platform and outsourcing products.

| | 2013 | | | | 2012 | | | | | |

| Hardware | $ | 59,357 | | | $ | 63,122 | | | (6 | )% |

Although there will be continuing fluctuations, we expect an overall decreasing trend in hardware sales due to the change in sales mix towards outsourcing contracts (which typically do not include hardware) and the deflationary trend of computer prices generally.

| | 2013 | | | | 2012 | | | | | |

| Cost of License | $ | 4,824 | | | $ | 6,111 | | | (21 | )% |

| Cost of support and service | $ | 603,920 | | | $ | 551,285 | | | 10 | % |

| Cost of hardware | $ | 43,650 | | | $ | 45,983 | | | (5 | )% |

| TOTAL COST OF SALES | $ | 652,394 | | | $ | 603,379 | | | 8 | % |

| TOTAL GROSS PROFIT | $ | 476,992 | | | $ | 423,730 | | | 13 | % |

Cost of license consists of the direct costs of third party software.

Sales of third party software products decreased compared to last year, leading to lower related costs and slightly increased gross profit margins.

Gross profit margins in support and service increased due to economies of scale realized from increased revenues, particularly in electronic payment services.

For the fiscal year, margins have decreased slightly, being impacted by reduced sales of higher margin products related to hardware upgrades.

| | 2013 | | | | 2012 | | | | | |

retention.

Income from continuing operations has grown from $105,287 in fiscal 2008 to $154,984 in fiscal 2012.

Our three most recent acquisitions were completed in fiscal 2010.

All of these acquisitions were accounted for using the purchase method of accounting and our consolidated financial statements include the results of operations of the acquired companies from their respective acquisition dates.

We move into fiscal 2013 with cautious optimism following strong fourth quarter fiscal 2012 results.

Cost of license depends greatly on third party reseller agreement software vendor costs.

2011.

FISCAL 2011 COMPARED TO FISCAL 2010

In fiscal 2011, revenues increased 16% or $130,311 compared to the prior year due primarily to strong organic growth and the prior year acquisitions of Goldleaf Financial Solutions, Inc. (“GFSI”), PEMCO Technology Services, Inc. (“PTSI”) and iPay Technologies Holding Company, LLC (“iPay”).

During fiscal 2011, the Company’s management continued to focus on cost management that, when combined with the growth in revenue, resulted in a 17% increase in net income.

Slow recovery from the US financial crisis remains a primary concern as it continues to threaten our customers and our industry.

The profits of many financial institutions remain low and this has resulted in some reduction of demand for new products and services.

During the past two years, a number of financial institutions have failed or been subject to government intervention.

To date, such actions have not materially impacted our revenue or results of operations.

In each of the past two years, approximately 1% of all financial institutions in the United States have closed or merged due to regulatory action.

We believe that the number of regulatory actions will continue to decline through fiscal 2012, absent a significant downturn in the economy.

The increase in bank failures and forced consolidations has been offset to some extent by a general decline in the level of acquisition activity among financial institutions.

A consolidation can benefit us when a newly combined institution is processed on our platform, or elects to move to one of our platforms, and can negatively impact us when a competing platform is elected.

Consolidations and acquisitions also positively impact our financial results in the short-term due to early termination fees which are generally provided for in multi-year outsourced contracts.

These fees are primarily generated when an existing outsourced client is acquired by another financial institution and can vary from period to period based on the number and size of clients that are acquired and how early in the contract term the contract is terminated.

We generally do not receive contract termination fees when a financial institution is subject to a government action or from a customer that has selected in-house processing.

Despite the difficult economic climate, we remain cautiously optimistic, with increasing portions of our business coming from recurring revenue, increases in backlog and an encouraging sales pipeline.

Our customers will continue to face regulatory and operational challenges which our products and services address, and in these times they have an even greater need for some of our solutions that directly address institutional profitability and efficiency.

We continue to have a strong balance sheet, access to extensive lines of credit, and an unwavering commitment to superior customer service, and we believe that we are well positioned to address current opportunities as well as those which will arise as the economic recovery strengthens.

Our cautious optimism was expressed through our acquisitions of GFSI, PTSI and iPay during fiscal 2010 and these acquisitions, the three largest in our Company’s history, combined with our existing solutions present us with opportunities to extend our customer base and produce returns for our stockholders.

| | 2011 | | | | 2010 | | | | | |

| License | $ | 53,067 | | | $ | 52,225 | | | 2 | % |

The increase in license revenue for the current year is primarily due to increased organic revenue from our Alogent® products (our suite of deposit and image capture products targeted at large financial institutions) and an additional quarter of revenues from GFSI (acquired in the second quarter of fiscal 2010).

This increase has been partially offset by decreases in our core software and imaging software license revenues, for which the average deal size was smaller compared to a year ago.

We believe our customers are continuing to postpone major capital investments in technology, including software, due to the slowly recovering economy.

agreement.

Our outsourced delivery does not require our customers to make a large, up-front capital investment in license fees.

| Support and service | $ | 852,253 | | | $ | 720,504 | | | 18 | % |

| Total Increase | $ | 131,749 | | | | | | |

In-house support and other services revenue increased as the acquisition of GFSI contributed additional revenue of $5,648 compared to a year ago.

Electronic payment services includes ATM, debit and credit card transaction processing, online bill payment services, remote deposit capture and transaction processing services, with revenues being primarily derived from transaction fees typically under five-year service contracts with our customers.

The revenue growth is attributable to the acquisitions of GFSI, PTSI and iPay, which combined to add $68,663 during the current year, and organic revenue growth within electronic payment services, excluding the effects of the acquisitions, continues to be strong with an increase of 12% over the prior fiscal year.

Outsourcing services are performed through our data and item processing centers, with revenues primarily derived from monthly usage or transaction fees typically under five-year service contracts with our customers.

The increase in implementation services revenue is primarily related to acquisition related revenues of $2,683 for GFSI (acquired in the second quarter of fiscal 2010) and increased revenue from merger conversions of $3,754 for existing customers that acquired other financial institutions.

| Hardware | $ | 61,577 | | | $ | 63,857 | | | (4 | )% |

We have no outstanding debt with variable interest rates as of June 30, 2013 and are therefore not currently exposed to interest risk.

Based on our outstanding debt with variable interest rates as of June 30, 2012, a 1% increase in our borrowing rate would increase annual interest expense in fiscal 2013 by less than $1,300.

Today, the Company’s extensive array of products and services includes processing transactions, automating business processes, and managing information for more than [removed: 11,900] [added: 11,300] financial institutions and diverse corporate entities.

JHA provides its products and services through three [removed: marketed] [added: business] brands:

| • | Jack Henry Banking is a leading provider of integrated data processing systems to [removed: more than 1,330] [added: almost 1,300] banks ranging from [removed: de novo or start-up] [added: community] institutions to mid-tier banks with assets of up to $30 billion. Our banking solutions support both in-house and outsourced operating environments with three functionally distinct core processing platforms and more than 100 integrated complementary solutions. |

| • | Symitar is a leading provider of core data processing solutions for credit unions of all sizes, with over [removed: 750] [added: 760] credit union customers. Symitar markets two functionally distinct core processing platforms and more than 50 integrated complementary solutions that support both in-house and outsourced operating environments. |

The majority of our revenue is derived from recurring [removed: outsourcing fees,] transaction processing fees, [removed: and support and service] [added: outsourcing] fees that generally have contract terms of five years or [removed: greater.][added: greater, and support and service fees.]

[removed: JHA’s gross revenue] [added: This] has [removed: grown] [added: increased] from $742.9 million [removed: in fiscal 2008 to $1,027.1 million in] [added: at the end of] fiscal [removed: 2012,] [added: 2008,] representing a compound annual growth rate during this challenging five-year period of [removed: 7] [added: 9] percent.

Net income from continuing operations has grown from $105.3 million to [removed: $155.0] [added: $176.6] million during this same five-year period, [removed: representing a compound]

[added: representing a compound] annual growth rate of [removed: 8] [added: 11] percent.

Information regarding the classification of our business into separate segments serving the banking and credit union industries is set forth in Note [removed: 13] [added: 12] to the Consolidated Financial Statements (see Item 8).

According to the Federal Deposit Insurance Corporation (“FDIC”), there were more than [removed: 7,300] [added: 7,000] commercial banks and savings institutions in this asset range as of December 31, [removed: 2011.][added: 2012.]

Jack Henry Banking currently supports [removed: over 1,330] [added: almost 1,300] of these banks with its core information processing platforms and complementary products and services.

According to the Credit Union National Association (“CUNA”), there were [removed: more than 7,300] [added: approximately 7,100] domestic credit unions as of December 31, [removed: 2011.][added: 2012.]

Symitar currently supports [removed: nearly 750] [added: over 760] of these credit unions with core information processing platforms and complementary products and services.

ProfitStars currently supports [removed: nearly] [added: approximately] 11,000 institutions with specialized solutions for generating additional revenue and growth, increasing security, mitigating operational risks, and controlling operating costs.

The FDIC reports the number of commercial banks and savings institutions declined [removed: 15] [added: 17] percent from the beginning of calendar year 2008 to the end of calendar year [removed: 2011.][added: 2012.]

Although the number of banks declined at a [removed: 3] [added: 4] percent compound annual rate during this period, aggregate assets increased at a compound annual rate of [removed: 5] [added: 4] percent and totaled [removed: $12.6] [added: $13.4] trillion as of December 31, [removed: 2011.][added: 2012.]

Comparing calendar years [removed: 2011] [added: 2012] to [removed: 2010, new bank charters decreased 73 percent and] [added: 2011,] mergers increased [removed: 1] [added: 5] percent.

CUNA reports the number of credit unions also declined [removed: 15] [added: 16] percent from the beginning of calendar year 2008 to the end of calendar year [removed: 2011.][added: 2012.]

Although the number of credit unions declined at a 3 percent compound annual rate during this period, aggregate assets increased at a compound annual rate of 6 percent and totaled [removed: $982.1 billion] [added: $1.0 trillion] as of December 31, [removed: 2011.][added: 2012.]

JHA’s extensive product and service offering enables diverse financial institutions to capitalize on these business [added: opportunities and respond to these business challenges.]

JHA’s mission is to protect and increase the value of its stockholders' investment by providing quality products and services to our [removed: customers by:][added: customers.]

[removed: Focused Diversification] Acquisition Strategy

| • | [removed: Expanded] [added: Expand] our base of core [removed: financial institution customers,] [added: system customers;] |

| • | [removed: Expanded our suite of complementary] [added: Provide] products and services that [removed: were cross] [added: can be] sold to existing [removed: customers,] [added: core customers and outside our base; and /or] |

| • | [removed: Jack Henry Banking] [added: Symitar] supports [removed: commercial banks] [added: credit unions of all sizes] with information and transaction processing platforms that provide enterprise-wide automation. Its solutions [removed: encompass three] [added: include two] functionally distinct core processing systems and more than [removed: 100] [added: 50] complementary solutions, including business intelligence and [removed: bank] [added: credit union] management, [removed: retail] [added: member] and [added: member] business [removed: banking, internet] [added: services, Internet] banking and [removed: electronic funds transfer (“EFT”),] [added: EFT,] risk management and protection, and item and document imaging solutions. Our [removed: banking] [added: credit union] solutions [added: also] have state-of-the-art functional capabilities, and we can provide the hardware required by each software system. Our [removed: banking] [added: credit union] solutions can be delivered in-house or through outsourced implementation, and are [added: also] backed by [removed: a] [added: our] company-wide commitment to provide exceptional personal service. [removed: Jack Henry Banking is a recognized market leader,] [added: Symitar] currently [removed: supporting nearly 1,330 banks with its technology platforms.] [added: supports over 760 credit union customers.] |

| • | ProfitStars is a leading provider of specialized products and services assembled through our focused diversification acquisition strategy. These solutions are compatible with a wide variety of information technology platforms and operating environments, and include proven solutions for generating additional revenue and growth, increasing security and mitigating operational risks, and/or controlling operating costs. ProfitStars’ products and services [removed: are enhancing] [added: enhance] the performance of financial services organizations of all asset sizes and charters, and diverse corporate entities with [removed: nearly] [added: approximately] 11,000 domestic and international customers. These distinct products and services can be implemented individually or as solution suites to address specific business problems and enable effective responses to dynamic industry trends. |

These core systems are available for in-house installation at customer [removed: sites] [added: sites,] or financial institutions can outsource ongoing information processing to [removed: JHA based on the core processing solution most compatible with their specific operational requirements.][added: JHA.]

| • | SilverLake® is a robust IBM® System i™-based system primarily designed for commercial-focused banks with assets ranging from $500 million to $30 billion. However, [removed: an increasing number of] [added: some] progressive smaller [removed: banks, including de novo, or] [added: banks and] recently chartered start-up [removed: banks, are now selecting] [added: banks also select] SilverLake. This system has been implemented by over 420 banks, and now automates approximately 6 percent of the domestic banks with assets less than $30 billion. |

| • | CIF 20/20® is a parameter-driven, easy-to-use system that now supports [removed: nearly 690] [added: over 650] banks ranging from de novo institutions to those with assets exceeding $2 billion. CIF 20/20 is the most widely used IBM System i-based core processing system in the community bank market. |

| • | Core Director® is a Windows®-based, client/server system that now supports over [removed: 220] [added: 210] banks ranging from de novo institutions to those with assets exceeding $1 billion. Core Director is a cost-efficient operating platform and provides intuitive point-and-click operation. |

| • | Episys® is a robust IBM System p™-based system primarily designed for credit unions with more than $50 million in assets. It has been implemented by over [removed: 570] [added: 580] credit unions and is ranked as the system implemented by more credit unions with assets exceeding $25 million than any other alternative. |

| • | Cruise® is a Windows-based, client/server system designed primarily for credit unions with less than $50 million in assets. It has been implemented by [removed: more than] [added: almost] 180 credit unions, is cost-efficient, and provides intuitive point-and-click, drag-and-drop operation. |

[removed: In-house customers generally] license our core software systems under a standard license agreement that provides a fully paid, nonexclusive, nontransferable right to use the software on a single computer at a single location.

Our [added: core] outsourcing services are provided through a national network of [added: four] data centers [added: located] in [removed: five] [added: three] physical [removed: locations and four image-enabled item processing centers.][added: locations.]

The Company’s Industry Research department solicits customer guidance on the business solutions they need, [removed: formally] evaluates available solutions and competitive offerings, and manages the introduction of new product offerings.

[removed: While it is not essential, the] [added: The] majority of our core bank and credit union customers contract with us for implementation [added: and training services in connection with their in-house systems.]

[removed: Know-It-All Education supports distinct learning preferences with a variety of delivery channels,] including classroom-based courses offered in JHA’s regional training centers, Internet-based live instruction, eLearning courses, on-site training, and train-the-trainer programs.

| • | Sophisticated support tools, resources, and technology; [removed: and] |

| • | A best practices methodology developed and refined through the company-wide, day-to-day experience supporting more than [removed: 11,900] [added: 11,300] diverse clients. |

[removed: JHA’s] [added: | • | Broad] experience converting diverse banks and credit unions to our core platforms from every competitive [removed: platform also provides highly effective change management and control processes.][added: platform; |]

JHA ended fiscal 2013 with $1,129.4 million gross revenue.

There were no new bank charters issued in calendar year 2012, compared to 3 in calendar 2011.

We perform this mission by:

We have a disciplined approach to acquisitions and have been successful in supplementing our organic growth with strategic acquisitions, including 27 material acquisitions since the end of fiscal 1999.

We continue to explore acquisitions that have the potential to:

| • | Expand our suite of complementary products and services; |

| • | Provide selective opportunities to sell outside our traditional markets in the financial services industry. |

We have not completed an acquisition since fiscal year 2010.

After 37 years in business we have very few gaps in our product line, so it is increasingly difficult to find proven products or services that would enable our clients and prospects to better optimize their business opportunities or solve specific operational issues.

in addition, we see few acquisition opportunities that would expand our market or enable our entry into adjacent markets within the financial services industry that are fairly priced or that we could assimilate into our company without material distractions.

We have a solid track record of executing acquisitions from both a financial and operational standpoint and we will continue to pursue acquisition opportunities that support our strategic direction, complement and accelerate our organic growth, and generate long-term profitable growth for our shareholders.

Until we identify appropriate acquisition opportunities, we will continue to find alternative ways to leverage our cash position to the benefit of our shareholders, such as repurchases of JKHY stock and payment of dividends.

Our three most recent material acquisitions were:

| • | Jack Henry Banking supports commercial banks with information and transaction processing platforms that provide enterprise-wide automation. We have three functionally distinct core bank processing systems and more than 100 complementary solutions, including business intelligence and bank management, retail and business |

banking, internet banking and electronic funds transfer (“EFT”), risk management and protection, and item and document imaging solutions.

Our banking solutions have state-of-the-art functional capabilities, and we can provide the hardware required by each software system.

Our banking solutions can be delivered in-house or through outsourced implementation, and are backed by a company-wide commitment to provide exceptional personal service.

Jack Henry Banking is a recognized market leader, currently supporting almost 1,300 banks with its technology platforms.

In-house customers generally

We also provide image item processing services from two host/archive sites and several key entry and balancing locations throughout the country.

We print and mail customer statements for financial institutions from two regional printing and rendering centers.

Know-It-All Education supports distinct learning preferences with a variety of delivery channels,

| • | Highly effective change management and control processes; and |

These examinations cover a wide variety of subjects, including system development, functionality, reliability, and security, as well as disaster preparedness and business recovery planning.

| | |

| --- | --- |

opportunities and respond to these business challenges.

JHA’s acquisition strategy, which complements and accelerates our organic growth, focuses on successful companies that provide in-demand products and services, excellent customer relationships, and strong management teams and employee bases.

Historically, our acquisition strategy focused on companies that:

| • | Enabled our entry into adjacent markets within the financial services industry; and/or |

| • | Provided additional outsourcing capabilities/opportunities. |

In 2004, we adopted our focused diversification acquisition strategy and began acquiring companies and highly specialized products that are:

| • | Sold to existing core customers; |

| • | Sold outside JHA’s base of core bank and credit union customers to financial services organizations of all charters and asset sizes; |

| • | Selectively sold outside the financial services industry to diverse corporate entities; and |

| • | Selectively sold internationally. |

Since our focused diversification strategy was adopted, JHA has completed 19 acquisitions that support it and assembled three distinct product brands that enable users to:

| • | Generate additional revenue and growth opportunities, |

| • | Increase security and mitigate operational risks, and /or |

| • | Control operating costs. |

These products and services enable us to expand our reach well beyond our traditional markets with solutions that are appropriate for virtually any financial services organization, including thousands of institutions that we previously did not sell to.

Following are the acquisitions that have been made in the last five fiscal years to support JHA’s focused diversification:

| 2008 | AudioTel | Check and document imaging and electronic banking |

| 2008 | Gladiator Technology | Information Technology Security Services |

| • | Symitar supports credit unions of all sizes with information and transaction processing platforms that provide enterprise-wide automation. Its solutions include two functionally distinct core processing systems and more than 50 complementary solutions, including business intelligence and credit union management, member and member business services, Internet banking and EFT, risk management and protection, and item and document imaging solutions. Our credit union solutions also have state-of-the-art functional capabilities, and we can provide the hardware required by each software system. Our credit union solutions can be delivered in-house or through outsourced implementation, and are also backed by our company-wide commitment to provide exceptional personal service. |

As part of ProfitStars, iPay Technologies, our most recent acquisition, provides a configurable electronic payments platform and turnkey online bill payment solutions that can integrate with any online banking platform.

Hardware sales support our software systems and include non-JHA products that we re-market.

and training services in connection with their in-house systems.

Jack Henry Banking also has been successfully selling its core and complementary solutions to a significant number of the de novo banks chartered in recent years.

for our primary trademarks.

NetTeller, ProfitStar’s Teleweb, and MemberConnect™ online solutions, and business recovery services through Centurion Disaster Recovery.

Information with respect to our legal proceedings may be found in Note 6 to the Financial Statements in Item 8, which is incorporated herein by reference.

We are subject to various routine legal proceedings and claims arising in the ordinary course of business.

We do not expect that the results in any of these legal proceedings will have a material adverse effect on our business, financial condition, results of operations or cash flows.

10-K 1 [removed: jkhy-2012630x10k.htm] [added: jkhy-2013630x10k.htm] FORM [removed: 10K] [added: 10-K] FOR FISCAL YEAR ENDED JUNE 30, [removed: 2012][added: 2013]

| | For the fiscal year ended June 30, [removed: 2012] [added: 2013] |

| Large accelerated filer [added: |] \[X\] | | Accelerated filer [added: |] \[ \] |

| Non-accelerated filer [added: |] \[ \] | (Do not check if a smaller reporting company) | Smaller reporting company [added: |] \[ \] |

As of August [removed: 22, 2012,] [added: 21, 2013,] the Registrant had [removed: 86,151,011] [added: 85,268,567] shares of Common Stock outstanding ($0.01 par value).

On December 31, [removed: 2011,] [added: 2012,] the aggregate market value of the Common Stock held by persons other than those who may be deemed affiliates of Registrant was [removed: $2,766,705,073] [added: $3,300,462,978] (based on the average of the reported high and low sales prices on NASDAQ on December 31, [removed: 2011).][added: 2012).]

Portions of the Company's Notice of Annual Meeting of Stockholders and Proxy Statement for its [removed: 2012] [added: 2013] Annual Meeting of Stockholders (the "Proxy Statement"), to the Table of Contents below, are incorporated by reference into Part II, Item 5 and into Part III of this Report.

| ITEM 1. | BUSINESS | [removed: [4](#s32D920D990DB3E17D4E6573E3C8DABA6)] [added: [4](#sB6EAB17F37A13B5E20BD862722A6E7F1)] |

| ITEM 1A. | RISK FACTORS | [removed: [12](#sCD7A0AC6E176575A2AA25744C184B031)] [added: [12](#sBDC0BB9DD3371F64B8DA862722D8E07D)] |

| ITEM 1B. | UNRESOLVED STAFF COMMENTS | [removed: [14](#s4194C5D4675689F636CA5745383C3750)] [added: [14](#sB785ABBABBACDB37859F862722F67958)] |

| ITEM 2. | PROPERTIES | [removed: [14](#s3A4B5EB2E6D38281C0465745EB317B04)] [added: [14](#sD9295AA5853A9FEC3387862723289B0E)] |

| ITEM 3. | LEGAL PROCEEDINGS | [removed: [15](#s1C2202B30AFF94F4B841574717B4F786)] [added: [15](#s8A8FDE6101765D30C36986272346E66D)] |

| ITEM 4. | MINE SAFETY DISCLOSURES | [removed: [15](#s1888AA5E361510490EDB576814BAE748)] [added: [15](#s4785AFA3CFAE84C9987986272378F972)] |

| ITEM 5. | MARKET FOR REGISTRANT'S COMMON EQUITY, RELATED STOCKHOLDER MATTERS AND ISSUER PURCHASES OF EQUITY SECURITIES | [removed: [15](#s59AAC66D7D477B22B8CA576D03E33B47)] [added: [15](#s17A66D7C69BC84D3271D86271E469FFF)] |

| ITEM 6. | SELECTED FINANCIAL DATA | [removed: [17](#s985BD9DB2F265D5C188A576D9015B1D7)] [added: [17](#s9D1526EB234DFE1A5C98862723FAA5FC)] |

| ITEM 7. | MANAGEMENT'S DISCUSSION AND ANALYSIS OF FINANCIAL CONDITION AND RESULTS OF OPERATIONS | [removed: [17](#sF521317626899B8FCC8956849ADBD5B4)] [added: [17](#s2C487D2580265351741E86272422680C)] |

| ITEM 7A. | QUANTITATIVE AND QUALITATIVE DISCLOSURES ABOUT MARKET RISK | [removed: [30](#sE1A927487CC4AF1FBC9C56849C7F178B)] [added: [30](#s4E23FCFE2D45F711D05C8627258A0BFE)] |

| ITEM 8. | FINANCIAL STATEMENTS AND SUPPLEMENTARY DATA | [removed: [31](#s6635D69AEB094D11F38A56849883CD34)] [added: [31](#sF4A762EE9AC0058AC57F862725C6C04A)] |

| ITEM 9. | CHANGES IN AND DISAGREEMENTS WITH ACCOUNTANTS ON ACCOUNTING AND FINANCIAL DISCLOSURE | [removed: [58](#sA052A77306349BC8EBD6576C74019321)] [added: [56](#s440E36BC263139A19516862729EA4DEC)] |

| ITEM 9A. | CONTROLS AND PROCEDURES | [removed: [58](#s7BE285639743FBBD302156849C9DCD1B)] [added: [56](#s2CBFDF74D7C9F3B13E7B862729FE8F13)] |

| ITEM 9B. | OTHER INFORMATION | [removed: [58](#s0DBFD7E8413813C64E30576979F760CF)] [added: [56](#s77A09D1652C64C9C060386272A1C0F63)] |

| ITEM 10. | DIRECTORS, EXECUTIVE OFFICERS AND CORPORATE GOVERNANCE | [removed: [59](#s5E32D5D3EB247E8DD88957731690E9C5)] [added: [57](#s13EAF86DBBF8A582EA9886272A6C89DE)] |

| ITEM 11. | EXECUTIVE COMPENSATION | [removed: [59](#sBB22D93FED81F4CC181257736A29C02A)] [added: [57](#sC7700BE97B95F7347F1F86272AA81AA8)] |

| ITEM 12. | SECURITY OWNERSHIP OF CERTAIN BENEFICIAL OWNERS AND MANAGEMENT AND RELATED STOCKHOLDER MATTERS | [removed: [59](#s877A6264E7F61C00E3595776C4C3CBF9)] [added: [57](#s4F35BF269841ACD0B09F86272AC6360C)] |

| ITEM 13. | CERTAIN RELATIONSHIPS AND RELATED TRANSACTIONS, AND DIRECTOR INDEPENDENCE | [removed: [59](#sC0AB3F2BF1C1D9DA228357773D633402)] [added: [57](#s233EBB04339EE358CAED86272AF8EECA)] |

| ITEM 14. | PRINCIPAL ACCOUNTANT FEES AND SERVICES | [removed: [59](#sFD96FF8A05FE594B77FE57778F1BDFD7)] [added: [57](#sFC853ACA20F9130B4F4486272B167894)] |

| ITEM 15 | EXHIBITS AND FINANCIAL STATEMENT SCHEDULES | [removed: [59](#sC7F1BCD21C004A04585A56849CE3F86A)] [added: [57](#sF1822291AB55F16FAAE786272B66249F)] |

| | | | | |

| --- | --- | --- | --- | --- |

| | | | | |

| | | | | |

| | | |

| --- | --- | --- |

[removed: We have 39 leased office facilities in 21] states, which total approximately [removed: 374,000] [added: 378,000] square feet.

Of our facilities, the credit union segment uses office space totaling approximately [removed: 151,000] [added: 162,000] square feet in ten facilities.

The remainder of our leased and owned facilities, approximately [removed: 1,223,000] [added: 1,216,000] square feet of office space, is primarily devoted to serving our bank segment or supports our whole business.

We own [removed: four] [added: five] aircraft.

We primarily use our airplanes in connection with implementation, sales of systems and internal [added: requirements for day-to-day operations.]

We have 37 leased office facilities in 21

requirements for day-to-day operations.

| | | Fiscal [removed: 2012] [added: 2013] | | | | | | | | Fiscal [removed: 2011] [added: 2012] | | | | | | |

| Fourth Quarter | | $ | [removed: 34.76] [added: 48.24] | | | $ | [removed: 32.17] [added: 37.90] | | | $ | [removed: 34.17] [added: 34.76] | | | $ | [removed: 28.45] [added: 32.17] | |

| Third Quarter | | [removed: 35.37] [added: 46.31] | | | | [removed: 32.11] [added: 39.60] | | | | [removed: 33.94] [added: 35.37] | | | | [removed: 28.96] [added: 32.11] | | |

| Second Quarter | | [removed: 34.50] [added: 40.71] | | | | [removed: 27.33] [added: 37.12] | | | | [removed: 29.97] [added: 34.50] | | | | [removed: 25.35] [added: 27.33] | | |

| First Quarter | | [removed: 31.15] [added: 38.22] | | | | [removed: 24.41] [added: 33.92] | | | | [removed: 26.30] [added: 31.15] | | | | [removed: 23.19] [added: 24.41] | | |

Quarterly dividends per share paid on the common stock for the two most recent fiscal years ended June 30, [removed: 2012] [added: 2013] and [removed: 2011] [added: 2012] are as follows:

| | | Fiscal [removed: 2012] [added: 2013] | | | | Fiscal [removed: 2011] [added: 2012] | | |

| Fourth Quarter | | $ | [removed: 0.115] [added: 0.200] | | | $ | [removed: 0.105] [added: 0.115] | |

| Third Quarter | | [removed: 0.115] [added: 0.130] | | | | [removed: 0.105] [added: 0.115] | | |

| Second Quarter | | [removed: 0.105] [added: 0.115] | | | | [removed: 0.095] [added: 0.105] | | |

| First Quarter | | [removed: 0.105] [added: 0.115] | | | | [removed: 0.095] [added: 0.105] | | |

On August [removed: 22, 2012,] [added: 16, 2013,] there were approximately [removed: 43,000] [added: 54,000] holders of the Company’s common stock.

On that same date the last sale price of the common shares as reported on NASDAQ was [removed: $37.13] [added: $50.47] per share.

The following shares of the Company were repurchased during the quarter ended June 30, [removed: 2012:][added: 2013:]

The following chart presents a comparison for the five-year period ended June 30, [removed: 2012,] [added: 2013,] of the market performance of the Company’s common stock with the S & P 500 Index and an index of peer companies selected by the Company:

[removed: ][added: ]

| | [removed: 2007 | |] 2008 | | 2009 | | 2010 | | 2011 | | 2012 | | [added: 2013 | |]

This comparison assumes $100 was invested on June 30, [removed: 2007,] [added: 2008,] and assumes reinvestments of dividends.

Companies in the [removed: New] Peer Group are [added: ACI Worldwide, Inc.,] Bottomline Technology, Inc., Cerner [added: Corp., DST Systems, Inc., Euronet Worldwide, Inc., Fair Isaac Corp., Fidelity National]

[removed: Corp., DST Systems, Inc., Euronet Worldwide, Inc., Fair Isaac Corp., Fidelity National] Information Services, Inc., Fiserv, Inc., [removed: Online Resources Corp.,] SEI Investments Company, Telecommunications Systems, Inc., and Tyler Technologies Corp.

| April 1 - April 30, 2013 | — | | | $ | — | | | — | | | 4,140,316 | |

| May 1 - May 31, 2013 | 436,034 | | | 46.98 | | | | 436,034 | | | 8,704,282 | |

| June 1 - June 30, 2013 | 467,555 | | | 46.74 | | | | 467,555 | | | 8,236,727 | |

| Total | 903,589 | | | 46.86 | | | | 903,589 | | | 8,236,727 | |

(1) Stock repurchase authorizations approved by the Company's Board of Directors as of April 1, 2013 was 20.0 million shares.

This was increased by 5.0 million shares on May 3, 2013.

COMPARISON OF 5 YEAR CUMULATIVE TOTAL RETURN

Among Jack Henry & Associates, Inc., the S&P 500 Index, and a Peer Group

| JKHY | 100.00 | | 97.64 | | 114.10 | | 145.41 | | 169.58 | | 234.60 | |

| Peer Group | 100.00 | | 97.18 | | 109.28 | | 146.52 | | 171.16 | | 214.21 | |

| S & P 500 | 100.00 | | 73.79 | | 84.43 | | 110.35 | | 116.36 | | 140.32 | |

| April 1 - April 30, 2012 | — | | | $ | — | | | — | | | 5,583,981 | |

| May 1 - May 31, 2012 | 717,099 | | | 32.92 | | | | 717,099 | | | 4,866,882 | |

| June 1 - June 30, 2012 | 328,330 | | | 32.78 | | | | 328,330 | | | 4,538,552 | |

| Total | 1,045,429 | | | 32.88 | | | | 1,045,429 | | | 4,538,552 | |

(1) Purchases made under the stock repurchase authorization approved by the Company's Board of Directors on October 4, 2002 with respect to 3.0 million shares, increased by 2.0 million shares on April 29, 2005, by 5.0 million shares on August 28, 2006, by 5.0 million shares on February 4, 2008, and by 5.0 million shares on August 25, 2008.

| JKHY | 100.00 | | 84.98 | | 82.97 | | 96.96 | | 123.57 | | 144.10 | |

| Old Peer Group | 100.00 | | 73.12 | | 72.29 | | 76.75 | | 107.02 | | 126.72 | |

| New Peer Group | 100.00 | | 73.30 | | 71.10 | | 79.71 | | 106.69 | | 124.52 | |

| S & P 500 | 100.00 | | 86.88 | | 64.10 | | 73.35 | | 95.87 | | 101.09 | |

In fiscal year 2012, we changed our peer group of companies used for this analysis to maintain alignment with peer companies selected by our Compensation Committee for use in determining compensation for executive management.

Companies in the Old Peer Group are Bottomline Technology, Inc., Cerner Corp., DST Systems, Inc., Euronet Worldwide, Inc., Fair Isaac Corp., Fidelity National Financial, Inc., Fiserv, Inc., Online Resources Corp., S1 Corp., SEI Investments Company, Telecommunications Systems, Inc., and Tyler Technologies Corp.

| Income Statement Data | | [removed: 2012] [added: 2013] | | | | [removed: 2011] [added: 2012] | | | | [removed: 2010] [added: 2011] | | | | [removed: 2009] [added: 2010] | | | | [removed: 2008] [added: 2009] | | |

| Revenue (1) | | $ | [removed: 1,027,109] [added: 1,129,386] | | | $ | [removed: 966,897] [added: 1,027,109] | | | $ | [removed: 836,586] [added: 966,897] | | | $ | [removed: 745,593] [added: 836,586] | | | $ | [removed: 742,926] [added: 745,593] | |

| Income from continuing operations | | $ | [removed: 154,984] [added: 176,645] | | | $ | [removed: 137,471] [added: 154,984] | | | $ | [removed: 117,870] [added: 137,471] | | | $ | [removed: 103,102] [added: 117,870] | | | $ | [removed: 105,287] [added: 103,102] | |

| Basic net income per share, continuing operations | | $ | [removed: 1.79] [added: 2.05] | | | $ | [removed: 1.60] [added: 1.79] | | | $ | [removed: 1.39] [added: 1.60] | | | $ | [removed: 1.23] [added: 1.39] | | | $ | [removed: 1.19] [added: 1.23] | |

| Diluted net income per share, continuing operations | | $ | [removed: 1.78] [added: 2.04] | | | $ | [removed: 1.59] [added: 1.78] | | | $ | [removed: 1.38] [added: 1.59] | | | $ | [removed: 1.22] [added: 1.38] | | | $ | [removed: 1.17] [added: 1.22] | |

| Dividends declared per share | | $ | [removed: 0.44] [added: 0.56] | | | $ | [removed: 0.40] [added: 0.44] | | | $ | [removed: 0.36] [added: 0.40] | | | $ | [removed: 0.32] [added: 0.36] | | | $ | [removed: 0.28] [added: 0.32] | |

| Working capital | | $ | [removed: 66,406] [added: 35,627] | | | $ | [removed: (26,561] [added: 66,406] | [removed: )] | | $ | [removed: (51,283] [added: (26,561] | ) | | $ | [removed: 15,239] [added: (51,283] | [added: )] | | $ | [removed: (11,418] [added: 15,239] | [removed: )] |

| Total assets | | $ | [removed: 1,619,492] [added: 1,629,155] | | | $ | [removed: 1,505,797] [added: 1,619,492] | | | $ | [removed: 1,560,560] [added: 1,505,797] | | | $ | [removed: 1,050,700] [added: 1,560,560] | | | $ | [removed: 1,021,044] [added: 1,050,700] | |

| Long-term debt | | $ | [removed: 106,166] [added: 7,366] | | | $ | [removed: 127,939] [added: 106,166] | | | $ | [removed: 272,732] [added: 127,939] | | | $ | [removed: —] [added: 272,732] | | | $ | [removed: 24] [added: —] | |

| Stockholders’ equity | | $ | [removed: 983,056] [added: 1,072,169] | | | $ | [removed: 879,776] [added: 983,056] | | | $ | [removed: 750,372] [added: 879,776] | | | $ | [removed: 626,506] [added: 750,372] | | | $ | [removed: 601,451] [added: 626,506] | |

| | [Report of Independent Registered Public Accounting [removed: Firm](#s716EF57CB29113D3AA665AFD9558B1C2) |] [added: Firm](#sF372B8262CFFE39A853A8627261664AA)] | [removed: [32](#s716EF57CB29113D3AA665AFD9558B1C2)] [added: [32](#sF372B8262CFFE39A853A8627261664AA)] |

| | [Management's Annual Report on Internal Control over Financial [removed: Reporting](#s916CB1C93B87D91D2D3B5AFDE3B4416A) |] [added: Reporting](#s671F71F0084F653365FC862726347FC4)] | [removed: [33](#s916CB1C93B87D91D2D3B5AFDE3B4416A)] [added: [33](#s671F71F0084F653365FC862726347FC4)] |

| | [Report of Independent Registered Public Accounting [removed: Firm](#sED212B32D63762486F985AFE203732FD) |] [added: Firm](#s834FC91F0351EE4B1D5D86272666AAAA)] | [removed: [34](#sED212B32D63762486F985AFE203732FD)] [added: [34](#s834FC91F0351EE4B1D5D86272666AAAA)] |

| | Financial Statements | | [removed: |]

| | [removed: |] [Consolidated Statements of [removed: Income,](#s4A12679135723D489BC15684921B6FA3)] [added: Income,](#sB4BD284195D36C653A9186271A68439B)] | |

| | [removed: | [Years] [added: Years] Ended June 30, [added: 2013,] 2012, [removed: 2011,] and [removed: 20](#s4A12679135723D489BC15684921B6FA3)10] [added: 2011] | [removed: [35](#s4A12679135723D489BC15684921B6FA3)] [added: [35](#sB4BD284195D36C653A9186271A68439B)] |

| | [removed: |] [Consolidated Balance [removed: Sheets,](#s0AE1C5944F5705C5F90956849207EABE)] [added: Sheets,](#s0D922F061A1FC14C718F86271A7C87E2)] | |

| | [removed: | [June] [added: June] 30, [removed: 2012] [added: 2013] and [removed: 201](#s0AE1C5944F5705C5F90956849207EABE)1] [added: 2012] | [removed: [36](#s0AE1C5944F5705C5F90956849207EABE)] [added: [36](#s0D922F061A1FC14C718F86271A7C87E2)] |

| | [removed: |] [Consolidated Statements of Changes in Stockholders' [removed: Equity,](#s525B42D19EE8DDD2043C5AFF00BFF6F3)] [added: Equity,](#s305DB83605E83C1E9E0D86271A4A01E0)] | |

| | [removed: | [Years] [added: Years] Ended June 30, [added: 2013,] 2012, [removed: 2011,] and [removed: 20](#s525B42D19EE8DDD2043C5AFF00BFF6F3)10] [added: 2011] | [removed: [37](#s525B42D19EE8DDD2043C5AFF00BFF6F3)] [added: [37](#s305DB83605E83C1E9E0D86271A4A01E0)] |

| | [removed: |] [Consolidated Statements of Cash [removed: Flows,](#s48C608EAED7D757E0008568491F34C5F)] [added: Flows,](#s4F397286893EDE6549FA86271A8621E9)] | |

| | [removed: | [Years] [added: Years] Ended June 30, [added: 2013,] 2012, [removed: 2011] and [removed: 20](#s48C608EAED7D757E0008568491F34C5F)10] [added: 2011] | [removed: [38](#s48C608EAED7D757E0008568491F34C5F)] [added: [38](#s4F397286893EDE6549FA86271A8621E9)] |

| | [removed: |] [Notes to Consolidated Financial [removed: Statements](#sF125E2037C9DAB0CFCCA56849937D1ED)] [added: Statements](#sFE13327E87C410EC7AC68627272ECAAD)] | [removed: [39](#sF125E2037C9DAB0CFCCA56849937D1ED)] [added: [39](#sFE13327E87C410EC7AC68627272ECAAD)] |

We have audited the accompanying consolidated balance sheets of Jack Henry & Associates, Inc. and subsidiaries (the “Company”) as of June 30, [removed: 2012] [added: 2013] and [removed: 2011,] [added: 2012,] and the related consolidated statements of income, changes in stockholders' equity, and cash flows for each of the three years in the period ended June 30, [removed: 2012.][added: 2013.]

Our responsibility is to express an opinion on [removed: these] [added: the] financial statements based on our audits.

In our opinion, such consolidated financial statements present fairly, in all material respects, the financial position of Jack Henry & Associates, Inc. and subsidiaries as of June 30, [removed: 2012] [added: 2013] and [removed: 2011,] [added: 2012,] and the results of their operations and their cash flows for each of the three years in the period June 30, [removed: 2012,] [added: 2013,] in conformity with accounting principles generally accepted in the United States of America.

We have also audited, in accordance with the standards of the Public Company Accounting Oversight Board (United States), the Company’s internal control over financial reporting as of June 30, [removed: 2012,] [added: 2013,] based on the criteria established in Internal [removed: Control—Integrated] [added: Control — Integrated] Framework issued by the Committee of Sponsoring Organizations of the Treadway Commission and our report dated August 27, [removed: 2012] [added: 2013] expressed an unqualified opinion on the Company’s internal control over financial reporting.

As of the end of the Company’s [removed: 2012] [added: 2013] fiscal year, management conducted an assessment of the effectiveness of the Company’s internal control over financial reporting based on the framework established in Internal Control—Integrated Framework issued by the Committee of Sponsoring Organizations of the Treadway Commission (COSO).

Based on this assessment, management has determined the Company’s internal control over financial reporting as of June 30, [removed: 2012] [added: 2013] was effective.

The Company’s internal control over financial reporting as of June 30, [removed: 2012] [added: 2013] has been audited by the Company’s independent registered public accounting firm, as stated in their report appearing on the next page.

We have audited the internal control over financial reporting of Jack Henry & Associates, Inc. and subsidiaries (the “Company”) as of June 30, [removed: 2012,] [added: 2013,] based on criteria established in Internal [removed: Control—Integrated] [added: Control — Integrated] Framework [added: (1992)] issued by the Committee of Sponsoring Organizations of the Treadway Commission.

In our opinion, the Company maintained, in all material respects, effective internal control over financial reporting as of June 30, [removed: 2012,] [added: 2013,] based on the criteria established in Internal [removed: Control—Integrated] [added: Control — Integrated] Framework [added: (1992)] issued by the Committee of Sponsoring Organizations of the Treadway Commission.

We have also audited, in accordance with the standards of the Public Company Accounting Oversight Board (United States), the consolidated financial statements as of and for the year ended June 30, [removed: 2012] [added: 2013] of the Company and our report dated August 27, [removed: 2012] [added: 2013] expressed an unqualified opinion on those financial statements.

| | [removed: 2012] [added: 2013] | | | | [removed: 2011] [added: 2012] | | | | [removed: 2010] [added: 2011] | | |

| License | $ | [removed: 54,811] [added: 54,818] | | | $ | [removed: 53,067] [added: 54,811] | | | $ | [removed: 52,225] [added: 53,067] | |

| Support and service | [removed: 909,176] [added: 1,015,211] | | | | [removed: 852,253] [added: 909,176] | | | | [removed: 720,504] [added: 852,253] | | |

| Hardware | [removed: 63,122] [added: 59,357] | | | | [removed: 61,577] [added: 63,122] | | | | [removed: 63,857] [added: 61,577] | | |

| Total revenue | [removed: 1,027,109] [added: 1,129,386] | | | | [removed: 966,897] [added: 1,027,109] | | | | [removed: 836,586] [added: 966,897] | | |

| Cost of license | [removed: 6,111] [added: 4,824] | | | | [removed: 6,285] [added: 6,111] | | | | [removed: 5,827] [added: 6,285] | | |

| Cost of support and service | [removed: 551,285] [added: 603,920] | | | | [removed: 515,917] [added: 551,285] | | | | [removed: 438,476] [added: 515,917] | | |

| Cost of hardware | [removed: 45,983] [added: 43,650] | | | | [removed: 45,361] [added: 45,983] | | | | [removed: 47,163] [added: 45,361] | | |

| Total cost of sales | [removed: 603,379] [added: 652,394] | | | | [removed: 567,563] [added: 603,379] | | | | [removed: 491,466] [added: 567,563] | | |

| GROSS PROFIT | [removed: 423,730] [added: 476,992] | | | | [removed: 399,334] [added: 423,730] | | | | [removed: 345,120] [added: 399,334] | | |

| Selling and marketing | [removed: 76,500] [added: 81,619] | | | | [removed: 68,061] [added: 76,500] | | | | [removed: 60,875] [added: 68,061] | | |

| Research and development | [removed: 60,876] [added: 63,202] | | | | [removed: 63,395] [added: 60,876] | | | | [removed: 50,820] [added: 63,395] | | |

| General and administrative | [removed: 50,119] [added: 66,624] | | | | [removed: 51,561] [added: 50,119] | | | | [removed: 51,172] [added: 51,561] | | |

| Total operating expenses | [removed: 187,495] [added: 211,445] | | | | [removed: 183,017] [added: 187,495] | | | | [removed: 162,867] [added: 183,017] | | |

| OPERATING INCOME | [removed: 236,235] [added: 265,547] | | | | [removed: 216,317] [added: 236,235] | | | | [removed: 182,253] [added: 216,317] | | |

| Interest income | [removed: 1,176] [added: 640] | | | | [removed: 125] [added: 1,176] | | | | [removed: 161] [added: 125] | | |

| Interest expense | [removed: (5,743] [added: (6,337] | | ) | | [removed: (8,930] [added: (5,743] | | ) | | [removed: (1,618] [added: (8,930] | | ) |

| | | |

| | | |

| | | |

| | | |

| | | |

| | | |

| | | |

| | | |

August 27, 2013

August 27, 2013

| Cash and cash equivalents | $ | 127,905 | | | $ | 157,313 | |

All of this amortization expense is included within Cost of support and service.

The total cost of treasury shares at June 30, 2013 is $402,082.

During fiscal 2013, the Company repurchased 1,302 treasury shares for $58,126.

The updated guidance adjusted the reporting requirements related to comprehensive income.

Adoption of these updates did not have any impact on the financial statements.

The provisions in this update were effective for the Company beginning July 1, 2012 and its adoption did not have any impact on the financial statements.

In July 2013, the FASB issued ASU No. 2013-11, Income Taxes.

The amendments update guidance on the financial statement presentation of an unrecognized tax benefit when a net operating loss carryforward, a similar tax loss, or a tax credit carryforward exists.

Level 1: inputs to the valuation are quoted prices in an active market for identical assets

Level 3: valuation is based on significant inputs that are unobservable in the market and the Company's own estimates of assumptions that we believe market participants would use in pricing the asset

| | 573,097 | | | | 518,159 | | | | | |

| Banking | 2013 | | | | 2012 | | |

| Beginning balance | $ | 403,949 | | | $ | 403,949 | |

| Goodwill, written off related to sale | (229 | | ) | | — | | |

| Ending balance | $ | 403,720 | | | $ | 403,949 | |

| Credit Union | | | | | | | |

| Beginning balance | $ | 129,571 | | | $ | 129,571 | |

| Goodwill, acquired during the year | — | | | | — | | |

| Ending balance | $ | 129,571 | | | $ | 129,571 | |

| | 2013 | | | | 2012 | | |

Our trade name assets have useful lives ranging from 5 to 20 years.

| | | | | | | | | | | | | | | | |

| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |

| | | | | | | | | | | | | | | | |

| 2014 | $ | 32,127 | | | $ | 14,337 | | | $ | 690 | | | $ | 47,154 | |

| 2015 | 26,696 | | | | 13,898 | | | | 672 | | | | 41,266 | | |

| 2016 | 19,665 | | | | 13,380 | | | | 472 | | | | 33,517 | | |

| 2017 | 10,852 | | | | 13,209 | | | | 472 | | | | 24,533 | | |

| 2018 | 3,349 | | | | 12,723 | | | | 472 | | | | 16,544 | | |

| | | | |

| --- | --- | --- | --- |

August 27, 2012

| | | | | | | | | | | | |

| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |

| Investments, at amortized cost | — | | | | 1,000 | | |

| Payment for acquisitions, net of cash acquired | — | | | | — | | | | (426,653 | | ) |

| Debt acquisition costs | — | | | | — | | | | (7,598 | | ) |

| CASH AND CASH EQUIVALENTS, BEGINNING OF PERIOD | $ | 63,125 | | | $ | 125,518 | | | $ | 118,251 | |

INVESTMENTS

The Company invests its cash that is not required for current operations primarily in U.S. government securities and money market accounts.

The Company has the positive intent and ability to hold its debt securities until maturity and accordingly, these securities are classified as held-to-maturity and are carried at historical cost adjusted for amortization of premiums and accretion of discounts.

Premiums and discounts are amortized and accreted, respectively, to interest income using the level-yield method over the period to maturity.

The held-to-maturity securities typically mature in less than one year.

Interest on investments in debt securities is included in income when earned.

At June 30, 2011, the amortized cost of held-to-maturity securities was $1,000.

Fair values of these securities did not differ significantly from amortized cost due to the nature of the securities and minor interest rate fluctuations during the periods.

on the face of the consolidated statements of income.

There were no repurchases of treasury stock in fiscal 2011.

The updated explanatory guidance on measuring fair value did not have a significant impact on our fair value calculations and no additional fair value measurements were required as a result of the update.

The FASB also issued ASU No. 2011-05, Comprehensive Income in June 2011, which is effective for the Company beginning July 1, 2012 and will be applied retrospectively.

The updated guidance requires non-owner changes in stockholders' equity to be reported either in a single continuous statement of comprehensive income or in two separate but consecutive statements, rather than as part of the statement of changes in stockholders' equity.

No changes in disclosure are anticipated as a result of the update.

Fair values for held-to-maturity securities are based on quoted market prices.

Level 1: observable inputs such as quoted prices in active markets

Level 3: unobservable inputs in which there is little or no market data, which requires the Company to develop its own assumptions

| | | Quoted Prices | | | | Significant | | | | Significant | | | | | | |

| | | in Active | | | | Observable | | | | Unobservable | | | | | | |

| | | Markets | | | | Other Inputs | | | | Inputs | | | | Total Fair | | |

| | | | | | | | | | | | | | | |

| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |

| | 518,159 | | | | 493,836 | | | | | | | | | |

There

were no changes in the carrying amount of goodwill in either of the periods presented.

Most of our trade name assets have been determined to have indefinite lives and are not amortized.

| Years Ending June 30, | Software | | | | Customer Relationships | | | | Total | | |

| 2013 | $ | 29,822 | | | $ | 14,522 | | | $ | 44,344 | |

| 2014 | 25,490 | | | | 14,522 | | | | 40,012 | | |

| 2015 | 19,656 | | | | 14,082 | | | | 33,738 | | |

| 2016 | 12,805 | | | | 13,565 | | | | 26,370 | | |

The Management’s Report on Internal Control over Financial Reporting required by this Item 9A is in Item 8, “Financial Statements and Supplementary Data.” Deloitte & Touche LLP has audited our internal control over financial reporting as of June 30, [removed: 2012;] [added: 2013;] their report is included in Item 8 of this Form 10K.

During the fiscal quarter ending June 30, [removed: 2012,] [added: 2013,] there has been no change in internal control over financial reporting that has materially affected, or is reasonably likely to affect, the Company’s internal control over financial reporting.

Attached as Exhibits 31.1 and 31.2 to this Annual Report on Form 10-K are certifications of the CEO and the CFO, which are required in [removed: accord] [added: accordance] with Rule 13a-14 of the Securities Exchange Act of 1934 (the Exchange Act).

Information required by Items 10, 11, 12, 13 and 14 of Part III is omitted from this report and will be filed within 120 days after the Company's June 30, 2013 fiscal year end in the definitive proxy statement for our 2013 Annual Meeting of Stockholders (the “Proxy Statement”).

See the information under the captions “Election of Directors”, “Corporate Governance”, [removed: “Audit Committee Report”, “Executive Officers and Significant Employees” and] “Section 16(a) Beneficial Ownership Reporting [removed: Compliance”] [added: Compliance”, and “Executive Officers and Significant Employees”] in the [removed: Company’s definitive] Proxy [removed: Statement for our 2012 Annual Meeting of Stockholders] [added: Statement,] which is incorporated herein by reference.

See the information under captions [removed: “Compensation Discussion and Analysis”, “Executive] [added: “Corporate Governance”, “Directors] Compensation”, “Compensation Committee Report”, [removed: “Corporate Governance”,] [added: “Compensation Discussion] and [removed: “Directors] [added: Analysis”, "Compensation and Risk", and “Executive] Compensation” in the [removed: Company’s definitive] Proxy [removed: Statement] [added: Statement,] which is incorporated herein by reference.

See the information under the captions “Stock Ownership of Certain Stockholders” and “Equity Compensation Plan Information” in the [removed: Company’s definitive] Proxy [removed: Statement] [added: Statement,] which is incorporated herein by reference.

See the information under the captions “Election of [removed: Directors”] [added: Directors - Director Independence”] and “Certain Relationships and Related Transactions” in the [removed: Company’s definitive] Proxy [removed: Statement] [added: Statement,] which is incorporated herein by reference.

See the information under the captions ”Audit Committee Report” and “Ratification of the Selection of [removed: the Company’s] Independent Registered Public Accounting Firm” in the [removed: Company’s definitive] Proxy [removed: Statement] [added: Statement,] which is incorporated herein by reference.

\- Consolidated Statements of Income for the years ended June 30, [removed: 2012, 2011] [added: 2013, 2012] and [removed: 2010][added: 2011]

\- Consolidated Balance Sheets as of June 30, [removed: 2012] [added: 2013] and [removed: 2011][added: 2012]

\- Consolidated Statements of Changes in Stockholders’ Equity for the years ended June 30, [removed: 2012, 2011] [added: 2013, 2012] and [removed: 2010][added: 2011]

\- Consolidated Statements of Cash Flows for the years ended June 30, [removed: 2012, 2011] [added: 2013, 2012] and [removed: 2010][added: 2011]

| [removed: 10.27] [added: 10.44] | [removed: The Company’s] [added: Form of Performance Shares Agreement Under the Jack Henry & Associates, Inc.] Restricted Stock Plan, attached as Exhibit [removed: 10.27] [added: 10.1] to the [removed: Company’s Annual] [added: Company's Current] Report on Form [removed: 10-K] [added: 8-K] filed September 12, [removed: 2006.] [added: 2012.] |

| [removed: 10.28] [added: 10.46] | [removed: The Company’s] [added: Jack Henry & Associates, Inc.] 2005 Non-Qualified Stock Option Plan, [added: as amended August 20, 2010,] attached as Exhibit [removed: 10.28] [added: 10.1] to the [removed: Company’s Annual] [added: Company's Quarterly] Report on [removed: Form 10-K] [added: form 10-Q] filed [removed: September 12, 2006.] [added: February 7, 2012.] |

| [removed: 10.41] [added: 10.45] | [removed: Amendment to] Jack Henry & [removed: Associates] [added: Associates,] Inc. [removed: Restricted Stock Plan dated August 20, 2010,] [added: 2012 Annual Incentive Plan, effective September 1, 2012 and approved by the stockholders on November 14, 2012,] attached as Exhibit 10.1 to the [removed: Company’s] [added: Company's] Current Report on Form 8-K filed [removed: August 24, 2010.] [added: November 16, 2012.] |

* Furnished with this report on Form 10-K are the following documents formatted in XBRL (Extensible Business Reporting Language): (i) the Consolidated Balance Sheets as of June 30, [removed: 2012] [added: 2013] and June 30, [removed: 2011,] [added: 2012,] (ii) the Consolidated Statements of Income for the years ended June 30, [removed: 2012, 2011] [added: 2013, 2012] and [removed: 2010,] [added: 2011,] (iii) the Consolidated Statements of Shareholders’ Equity for the years ended June 30, [removed: 2012, 2011] [added: 2013, 2012] and [removed: 2010,] [added: 2011,] (iv) the Consolidated Statements of Cash Flows for the years ended June 30, [removed: 2012, 2011] [added: 2013, 2012] and [removed: 2010,] [added: 2011,] and (v) Notes to Consolidated Financial Statements.

Pursuant to the requirements of Section 13 or 15(d) of the Securities Exchange Act of 1934, the registrant has duly caused this report to be signed on its behalf by the undersigned, thereunto duly authorized this 27th day of August, [removed: 2012.][added: 2013.]

| /s/ John F. Prim John F. Prim | Chairman of the Board, Chief Executive Officer and Director | August 27, [removed: 2012] [added: 2013] |

| /s/ Kevin D. Williams Kevin D. Williams | Chief Financial Officer and Treasurer (Principal Accounting Officer) | August 27, [removed: 2012] [added: 2013] |

| /s/ Wesley A. Brown Wesley A. Brown | Director | August 27, [removed: 2012] [added: 2013] |

| /s/ Matthew Flanigan Matthew Flanigan | Director | August 27, [removed: 2012] [added: 2013] |

| /s/ Marla Shepard Marla Shepard | Director | August 27, [removed: 2012] [added: 2013] |

| /s/ Tom H. Wilson, Jr Tom H. Wilson, Jr | Director | August 27, [removed: 2012] [added: 2013] |

| /s/ Jacqueline R. Fiegel Jacqueline R. Fiegel | Director | August 27, [removed: 2012] [added: 2013] |

| /s/ Thomas A. Wimsett Thomas A. Wimsett | Director | August 27, [removed: 2012] [added: 2013] |

| | |

| --- | --- |

| 10.3 | The Company’s 1995 Non-Qualified Stock Option Plan, attached as Exhibit 10.3 to the Company’s Annual Report on Form 10-K for the Year Ended June 30, 1996. |

| 10.9 | The Company’s 1996 Stock Option Plan, attached as Exhibit 10.9 to the Company’s Annual Report on Form 10-K for the Year Ended June 30, 1997. |

| 10.21 | Amendment to the Company’s 1996 Stock Option Plan, attached as Exhibit 10.1 to the Company’s Current Report on Form 8-K filed July 5, 2005. |

| 10.37 | Jack Henry & Associates, Inc. 1996 Stock Option Plan, as amended May 9, 2008, attached as Exhibit 10.37 to the Company’s Annual Report on Form 10-K filed August 29, 2008. |

| | | |

| /s/ Jerry D. Hall Jerry D. Hall | Executive Vice President and Director | August 27, 2012 |