Jack Henry & Associates (JKHY) 10-K/A risk factor changes: FY2014 vs FY2011

The Company's business and the results of its operations are affected by numerous factors and uncertainties, some of which are beyond our control.

The following is a description of some of the important risks and uncertainties that may cause the actual results of the Company's operations in future periods to differ from those expected or desired.

We have restated our prior consolidated financial statements, which may lead to additional risks and uncertainties, including loss of investor confidence and negative impacts on our stock price.

As discussed in Note 15 to our consolidated financial statements included in Item 8 of this Form 10-K/A, we have restated our consolidated financial statements as of and for the years ended June 30, 2014, 2013 and 2012 and for the quarterly periods within the fiscal years ended June 30, 2014 and 2013 (the "Restated Periods").

The determination to restate the financial statements for the Restated Periods was made by our Audit Committee upon management’s recommendation following the identification of errors related to our method of accounting for revenue from certain bundled software multi-element agreements.

Due to the errors, our management concluded that the Company's previously issued financial statements for the Restated Periods should no longer be relied upon.

Our Annual Report on Form 10-K for the year ended June 30, 2014 has been amended by this Amendment No. 1 on Form 10-K/A to, among other things, reflect the restatement of our financial statements for the Restated Periods, as discussed in Note 15 to our consolidated financial statements included in Item 8 of this Amendment No. 1 to Form 10-K.

As a result of these events, we have become subject to a number of additional costs and risks, including unanticipated costs for accounting and legal fees in connection with or related to the restatement and the risk of potential stockholder litigation.

If lawsuits are filed, we may incur additional substantial defense costs regardless of the outcome of such litigation.

Likewise, such events might cause a diversion of our management’s time and attention.

If we do not prevail in any such litigation, we could be required to pay substantial damages or settlement costs.

In addition, the restatement may lead to a loss of investor confidence and have negative impacts on the trading price of our common stock.

We have identified a material weakness in our internal control over financial reporting which could, if not remediated, result in additional material misstatements in our financial statements.

Our management is responsible for establishing and maintaining adequate internal control over our financial reporting, as defined in Rule 13a-15(f) under the Securities Exchange Act of 1934, as amended.

As disclosed in Item 9A of this Form 10-K/A, management identified a material weakness in our internal control over financial reporting based upon our identification of certain errors related to our method of accounting for revenue from certain bundled software multi-element agreements.

A material weakness is defined as a deficiency, or combination of deficiencies, in internal control over financial reporting, such that there is a reasonable possibility that a material misstatement of our annual or interim financial statements will not be prevented or detected on a timely basis.

As a result of this material weakness, our management concluded that the Company did not maintain effective internal control over financial reporting as of June 30, 2014.

Our Annual Report on Form 10-K for the year ended June 30, 2014 has been amended by this Amendment No. 1 on Form 10-K/A to, among other things, reflect the change in management's conclusion regarding the

effectiveness of our disclosure controls and procedures and internal control over financial reporting as of June 30, 2014, as discussed in Item 8 and Item 9A of this Form 10-K/A.

We are actively engaged in developing a remediation plan designed to address this material weakness.

If our remedial measures are insufficient to address the material weakness, or if additional material weaknesses or significant deficiencies in our internal control are discovered or occur in the future, our consolidated financial statements may contain material misstatements and we could be required to restate our financial results, which could materially and adversely affect the Company's business and results of operations or financial condition, restrict its ability to access the capital markets, require the Company to expend significant resources to correct the weaknesses or deficiencies, subject it to fines, penalties or judgments, harm its reputation or otherwise cause a decline in investor confidence.

Operational failure in our outsourcing facilities could expose us to damage claims, increase regulatory scrutiny and cause us to lose customers.

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

Our back-up systems and procedures may not prevent disruption, such as a prolonged interruption of our transaction processing services.

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

In 2012, we experienced a disruption to our operations at our Lyndhurst, NJ processing center as a result of Super Storm Sandy.

Any significant interruption of service could reduce revenue, have a negative impact on our reputation, result in damage claims, lead our present and potential customers to choose other service providers, and lead to increased regulatory scrutiny of the critical services we provide to financial institutions, with resulting increases in compliance burdens and costs.

Failures associated with payment transactions could result in financial loss.

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

We settle funds on behalf of financial institutions, other businesses and consumers and receive funds from clients, card issuers, payment networks and consumers on a daily basis for a variety of transaction types.

Transactions facilitated by us include debit card, credit card, electronic bill payment transactions, Automated Clearing House (“ACH”) payments and check clearing that supports consumers, financial institutions and other businesses.

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 financial as well as reputational loss to us.

In addition, we rely on various financial institutions to provide ACH services in support of funds settlement for certain of our products.

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.

In addition, we may issue credit to consumers, financial institutions or other businesses as part of the funds settlement.

A default on this credit by a counterparty could result in a financial loss to us.

Security problems could damage our reputation and business.

We rely on industry-standard encryption, network and Internet security systems, most of which we license from third parties, to provide the security and authentication necessary to effect secure transmission of data.

Our services and infrastructure are increasingly reliant on the Internet.

Computer networks and the Internet are vulnerable to unauthorized access, computer viruses and other disruptive problems such as denial of service attacks and other forms of cyber-terrorism.

The following section provides management's view of the financial condition and results of operations and should be read in conjunction with the Selected Financial Data, the audited Consolidated Financial Statements, and related notes included elsewhere in this report.

All of the financial information presented in this Item 7 has been revised to reflect the restatement of our consolidated financial statements more fully described in Note 15 - Restatement of Consolidated Financial Statements which is included in "Financial Statements and Supplementary Data" in Item 8 of this 2014 Amended Annual Report on Form 10-K/A.

OVERVIEW

Jack Henry & Associates, Inc. (JHA) is headquartered in Monett, Missouri, employs approximately 5,600 associates nationwide, and is a leading provider of technology solutions and payment processing services primarily for financial services organizations.

Its solutions serve nearly 11,300 customers and are marketed and supported through three primary brands.

Jack Henry Banking® supports banks ranging from community to mid-tier, multi-billion dollar institutions with information and transaction processing solutions.

Symitar® is a leading provider of information and transaction processing solutions for credit unions of all sizes.

ProfitStars® provides specialized products and services that enable financial institutions of every asset size and charter, and diverse corporate entities outside the financial services industry, to mitigate and control risks, optimize revenue and growth opportunities, and contain costs.

JHA's integrated solutions are available for in-house installation and outsourced and hosted delivery.

Each of our brands share the fundamental commitment to provide high quality business solutions, service levels that consistently exceed customer expectations, integration of solutions and practical new technologies.

The quality of our

solutions, our high service standards, and the fundamental way we do business typically foster long-term customer relationships, attract prospective customers, and have enabled us to capture substantial market share.

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 business brands.

We provide compatible computer hardware for our in-house installations and secure processing environments for our outsourced and hosted solutions.

We perform data conversions, software implementations, initial and ongoing customer training, and ongoing customer support services.

Our primary competitive advantage is customer service.

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 retention.

We consistently measure customer satisfaction using comprehensive annual surveys and random surveys we receive in our everyday business.

Dedicated surveys are also used to grade specific aspects of our customer experience, including product implementation, education, and consulting services.

The majority of our revenue is derived from recurring outsourcing fees and transaction processing fees that predominantly have contract terms of five years or greater at inception.

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

Less predictable software license fees and hardware sales complement our primary revenue sources.

We continually seek opportunities to increase revenue while at the same time containing costs to expand margins.

During the last five fiscal years, our revenues have grown from $832,777 in fiscal 2010 to $1,173,173 in fiscal 2014.

Income from continuing operations has grown from $116,722 in fiscal 2010 to $186,715 in fiscal 2014.

This growth has resulted primarily from internal expansion.

We have two reportable segments: bank systems and services and credit union systems and services.

The respective segments include all related license, support and service, and hardware sales along with the related cost of sales.

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

We are cautiously optimistic regarding ongoing economic improvement and expect our clients to continue investing in our products and services to improve their operating efficiencies and performance.

We anticipate that consolidation within the financial services industry will continue.

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

A detailed discussion of the major components of the results of operations follows.

All dollar amounts are in thousands and discussions compare fiscal 2014 to fiscal 2013 and compare fiscal 2013 to fiscal 2012.

RESULTS OF OPERATIONS

FISCAL 2014 COMPARED TO FISCAL 2013

In fiscal 2014, revenues increased 6% or $65,649 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 7% increase in gross profit.

Operating expenses decreased 2% for the year mainly due to $12,436 of expenses in the prior year related to the impact of Hurricane Sandy flooding on our Lyndhurst, New Jersey item processing center.

Provision for income taxes increased over the prior year.

10-K/A 1 [removed: jkhy2011q4-10ka.htm] [added: jkhy-2014630x10ka.htm] FORM [removed: 10K/A] [added: 10-K/A] FOR FISCAL YEAR ENDED JUNE 30, [removed: 2011][added: 2014]

[removed: UNITED STATES][added: UNITED STATES]

[removed: SECURITIES] [added: SECURITIES] AND EXCHANGE [removed: COMMISSION][added: COMMISSION]

[removed: Washington,] [added: WASHINGTON,] D.C. [removed: 20549][added: 20549]

[removed: FORM 10-K/A][added: FORM 10-K/A]

[removed: Amendment] [added: Amendment] No. [removed: 1][added: 1]

[removed: ANNUAL REPORT][added: ANNUAL REPORT]

[removed: PURSUANT] [added: PURSUANT] TO SECTION 13 OR [removed: 15(d)][added: 15(d)]

[removed: OF] [added: OF] THE SECURITIES EXCHANGE ACT OF [removed: 1934][added: 1934]

[removed: (Mark One)][added: (Mark One)]

[removed: \[X\]] [added: | (X) |] ANNUAL REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF [removed: 1934][added: 1934 |]

[added: | |] For the fiscal year ended June 30, [removed: 2011][added: 2014 |]

[removed: \[ \]] [added: | ( ) |] TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF [removed: 1934][added: 1934 |]

[added: | |] For the transition period from [removed: _______________] [added: ______________] to [removed: _______________][added: ________________ |]

[removed: JACK] [added: JACK] HENRY [removed: AND] [added: &] ASSOCIATES, [removed: INC.][added: INC.]

| [removed: Delaware] (State or [removed: other jurisdiction] [added: Other Jurisdiction] of [removed: incorporation or organization)] [added: Incorporation)] | | [removed: 43-1128385 (I.R.S.] [added: (I.R.S] Employer Identification No.) |

(Address of [removed: principal executive offices)][added: Principle Executive Offices)]

[removed: Registrant’s] [added: (Registrant’s] telephone number, including area [removed: code: (417) 235-6652][added: code)]

| [removed: Title of each class] Common Stock ($0.01 par value) | | [removed: Name of each exchange on which registered] NASDAQ Global Select Market |

Yes \[ [removed: X] \] No \[ [added: X] \]

Yes \[ [removed: X] \] No \[ [added: X] \]

Indicate by check mark if disclosure of delinquent filers pursuant to Item 405 of Regulation S-K is not contained herein, and will not be contained, to the best of registrant’s knowledge, in definitive proxy or information statements incorporated by reference in Part III of this Form [removed: 10-K] [added: 10-K/A] or any amendment to this Form [removed: 10-K.][added: 10-K/A.]

[added: |] Large [removed: Accelerated Filer \[ X \]] [added: accelerated filer | \[X\] | |] Accelerated [removed: Filer \[ \] Non-Accelerated Filer] [added: filer |] \[ \] [added: |]

As of August [removed: 22, 2011,] [added: 20, 2014,] the Registrant had [removed: 86,397,007] [added: 82,481,908] shares of Common Stock outstanding ($0.01 par value).

On December 31, [removed: 2010,] [added: 2013,] the aggregate market value of the Common Stock held by persons other than those who may be deemed affiliates of Registrant was [removed: $2,363,957,956] [added: $4,998,746,579] (based on the average of the reported high and low sales prices on NASDAQ on December 31, [removed: 2010).][added: 2013).]

[removed: DOCUMENTS] [added: DOCUMENTS] INCORPORATED BY [removed: REFERENCE][added: REFERENCE]

Portions of the Company's Notice of Annual Meeting of Stockholders and Proxy Statement for its [removed: 2011] [added: 2014] Annual Meeting of Stockholders (the "Proxy [removed: Statement"), to the Table of Contents below,] [added: Statement")] are incorporated by reference into Part II, Item 5 and into Part III of this Report.

[removed: EXPLANATORY NOTE][added: Explanatory Note]

This [removed: Amendment No. 1] [added: 2014 Amended Annual Report on Form 10-K/A] does not reflect [removed: any subsequent information or] events occurring after the [removed: original filing date of the Form 10-K] [added: Original Filing on August 27, 2014] or modify or update [removed: in any way] [added: those] disclosures [removed: made in] [added: affected by subsequent events, except for] the [removed: Form 10-K, as filed with] [added: effects of] the [removed: Securities and Exchange Commission on August 29, 2011.][added: restatement.]

[removed: PART IV][added: | PART I | | |]

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417-235-6652

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TABLE OF CONTENTS

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| | | Page Reference |

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| | EXPLANATORY NOTE | [4](#s22ff1a8efcd44e9fbd07a6059ead1551) |

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| ITEM 1A. | RISK FACTORS | [5](#s9cb5a089741f44e5b1bfe6ca02956afc) |

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| PART II | | |

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| ITEM 6. | SELECTED FINANCIAL DATA | [9](#sad7615131d9847f49f831355fb71d41d) |

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| ITEM 7. | MANAGEMENT'S DISCUSSION AND ANALYSIS OF FINANCIAL CONDITION AND RESULTS OF OPERATIONS | [10](#sc4688f1833d049209ea23a4417074589) |

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| ITEM 8. | FINANCIAL STATEMENTS AND SUPPLEMENTARY DATA | [24](#sBB10977B87D65C5FF5F77A36A42CC4A4) |

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| ITEM 9A. | CONTROLS AND PROCEDURES | [65](#sC550B1A6D31BCCE0FEDD7A36A8728588) |

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| PART IV | | |

OR

\[ \]

Smaller reporting Company \[ \]

This Amendment No. 1 to the Jack Henry & Associates, Inc. Annual Report on Form 10-K for the year ended June 30, 2011, which was filed with the Securities and Exchange Commission on August 29, 2011 (the “Form 10-K”), is being filed solely to amend the Form 10-K to furnish our XBRL interactive data files as Exhibit 101, as required by Rule 405 of Regulations S-T.

No changes have been made to the Form 10-K other than as described above.

Pursuant to Rule 406T of Regulation S-T, the interactive data files on Exhibit 101 hereto are deemed not filed or part of a registration statement or prospectus for purposes of Sections 11 or 12 of the Securities Act of 1933, as amended, are deemed not filed for purposes of Section 18 of the Securities Exchange Act of 1934, as amended, and otherwise are not subject to liability under those sections.

The selected financial information for the fiscal years ended June 30, 2014, 2013, and 2012 and as of June 30, 2014 and 2013, was derived from audited consolidated financial statements included in this amended filing and has been revised for the effects of the restatement more fully described in Note 15 - Restatement of Consolidated Financial Statements which is included in "Financial Statements and Supplementary Data" in Item 8 of this 2014 Amended Annual Report on Form 10-K/A.

The selected financial information for the years ended June 30, 2011 and 2010 and as of June 30, 2012, 2011 and 2010 was derived from previously audited consolidated financial statements not included in this filing; however, such financial information has been similarly revised for the effects of the restatement.

The following selected financial data should be read in conjunction with "Management's Discussion and Analysis of Financial Condition and Results of Operations" and the Consolidated Financial Statements and related notes thereto, especially as the information pertains to 2012, 2011 and 2010 activity.

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| Selected Financial Data | | | | | | | | | | | | | | | | | | | | |

| (In Thousands, Except Per Share Data) | | | | | | | | | | | | | | | | | | | | |

| | | YEAR ENDED JUNE 30, | | | | | | | | | | | | | | | | | | |

| Income Statement Data | | 2014 As Restated (2) | | | | 2013 As Restated (2) | | | | 2012 As Restated (2) (3) | | | | 2011 As Restated (3) | | | | 2010 As Restated (3) | | |

| Revenue (1) | | $ | 1,173,173 | | | $ | 1,107,524 | | | $ | 1,017,667 | | | $ | 946,394 | | | $ | 832,777 | |

| Income from continuing operations | | $ | 186,715 | | | $ | 167,610 | | | $ | 152,040 | | | $ | 128,394 | | | $ | 116,722 | |

| Basic net income per share, continuing operations | | $ | 2.20 | | | $ | 1.95 | | | $ | 1.76 | | | $ | 1.49 | | | $ | 1.38 | |

| Diluted net income per share, continuing operations | | $ | 2.19 | | | $ | 1.94 | | | $ | 1.74 | | | $ | 1.48 | | | $ | 1.37 | |

| Dividends declared per share | | $ | 0.840 | | | $ | 0.560 | | | $ | 0.440 | | | $ | 0.400 | | | $ | 0.360 | |

| Balance Sheet Data | | | | | | | | | | | | | | | | | | | | |

| Total deferred revenue | | $ | 492,868 | | | $ | 439,596 | | | $ | 409,139 | | | $ | 398,800 | | | $ | 358,811 | |

| Total assets | | $ | 1,680,703 | | | $ | 1,672,386 | | | $ | 1,655,652 | | | $ | 1,537,158 | | | $ | 1,586,168 | |

| Long-term debt | | $ | 3,729 | | | $ | 7,366 | | | $ | 106,166 | | | $ | 127,939 | | | $ | 272,732 | |

| Stockholders’ equity | | $ | 967,387 | | | $ | 1,015,816 | | | $ | 935,738 | | | $ | 835,403 | | | $ | 715,076 | |

(1) Revenue includes license sales, support and service revenues, and hardware sales, less returns and allowances.

(2) The effects of the restatement on the Company's consolidated balance sheets as of June 30, 2014 and 2013 and consolidated statements of income for the fiscal years ended June 30, 2014, 2013 and 2012 are described in the “Explanatory Note” immediately preceding Part I, Item 1A and Note 15, “Restatement of Consolidated Financial Statements,” in Notes to Consolidated Financial Statements of this Form 10-K/A.

(3) Selected Financial Data for the fiscal years ended June 30, 2012, 2011 and 2010 has also been restated to reflect adjustments related to the errors described in the “Explanatory Note” immediately preceding Part I, Item 1A of this Form 10-K.

The effects of the restatement on the Company's consolidated balance sheets as of June 30, 2012, 2011 and 2010 and consolidated statements of income for the fiscal years ended June 30, 2011 and 2010 are shown below.

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| | | YEAR ENDED JUNE 30, 2012 | | | | | | | | | | |

| Balance Sheet Data | | As Reported | | | | Effect of Restatement | | | | As Restated | | |

| Total deferred revenue | | $ | 296,000 | | | $ | 113,139 | | | $ | 409,139 | |

| Total assets | | $ | 1,619,492 | | | $ | 36,160 | | | $ | 1,655,652 | |

| Long-term debt | | $ | 106,166 | | | $ | — | | | $ | 106,166 | |

| Stockholders’ equity | | $ | 983,056 | | | $ | (47,318 | ) | | $ | 935,738 | |

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| | | YEAR ENDED JUNE 30, 2011 | | | | | | | | | | |

| Income Statement Data | | As Reported | | | | Effect of Restatement | | | | As Restated | | |

| Revenue (1) | | $ | 966,897 | | | $ | (20,503 | ) | | $ | 946,394 | |

| Income from continuing operations | | $ | 137,471 | | | $ | (9,077 | ) | | $ | 128,394 | |

Index to Financial Statements

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| | [Report of Independent Registered Public Accounting Firm](#sEBE01FB2D2028D1B5DF17A36D51F0FA5) | [25](#s9B0194BAA429F678BC417A36A48AC361) |

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| | [Management's Annual Report on Internal Control over Financial Reporting](#sEFF840270000E2F544A97A36D51FE169) (Revised) | [26](#sDDCB163979D66179715A7A36A4A9038D) |

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| | [Report of Independent Registered Public Accounting Firm](#s670B1E1EEA2AEF4978EB7A36D51F0706) | [27](#sD629847B6751896B25B57A36A4D86D4F) |

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| | Financial Statements | |

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| | [Consolidated Statements of Income,](#s33FC4FC45080B71C988A7A36D52F842D) | |

| | Years Ended June 30, 2014 (Restated), 2013 (Restated), and 2012 (Restated) | [29](#sEDBE1BE567A1C59B31C87A3699005F2C) |

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| | [Consolidated Balance Sheets,](#s45C5A9ECA91A6FEA53787A36D52F3D2C) | |

| | June 30, 2014 (Restated) and 2013 (Restated) | [30](#s340D1C759B0EF728460B7A3698F11EA9) |

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| | [Consolidated Statements of Changes in Stockholders' Equity,](#sDA01122CDEA9E33710AF7A36D52F82EA) | |

| | Years Ended June 30, 2014 (Restated), 2013 (Restated), and 2012 (Restated) | [31](#sB0F309BC88B77E0E55BD7A3697D7E023) |

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| | [Consolidated Statements of Cash Flows,](#s0E5EF84046619286930B7A36D52F1D73) | |

| | Years Ended June 30, 2014 (Restated), 2013 (Restated), and 2012 (Restated) | [32](#s7F1819243D778C4B25F67A3697E7EE32) |

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| | [Notes to Consolidated Financial Statements](#s48C94008ED6CB53E7BF57A36D53EB7E7) | [34](#s579EB61F1F9BD06C52187A36A5A3F5BF) |

Financial Statement Schedules

There are no schedules included because they are not applicable or the required information is shown in the consolidated financial statements or notes thereto.

REPORT OF INDEPENDENT REGISTERED PUBLIC ACCOUNTING FIRM

To the Board of Directors and Stockholders of

Jack Henry & Associates, Inc.

Monett, Missouri

We have audited the accompanying consolidated balance sheets of Jack Henry & Associates, Inc. and subsidiaries (the “Company”) as of June 30, 2014 and 2013, 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, 2014.

These financial statements are the responsibility of the Company’s management.

Our responsibility is to express an opinion on these financial statements based on our audits.

We conducted our audits in accordance with the standards of the Public Company Accounting Oversight Board (United States).

Those standards require that we plan and perform the audit to obtain reasonable assurance about whether the financial statements are free of material misstatement.

An audit includes examining, on a test basis, evidence supporting the amounts and disclosures in the financial statements.

An audit also includes assessing the accounting principles used and significant estimates made by management, as well as evaluating the overall financial statement presentation.

We believe that our audits provide a reasonable basis for our opinion.

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, 2014 and 2013, and the results of their operations and their cash flows for each of the three years in the period ended June 30, 2014, in conformity with accounting principles generally accepted in the United States of America.

In connection with the filing of the Company's Annual Report on Form 10-K for the fiscal year ended June 30, 2014 on August 27, 2014, an evaluation was carried out under the supervision and with the participation of our management, including the Company's Chief Executive Officer ("CEO") and Chief Financial Officer ("CFO"), of the effectiveness of the design and operation of our disclosure controls and procedures pursuant to Exchange Act Rules 13a-15 and 15d-15.

Based upon that evaluation, the CEO and CFO concluded that our disclosure controls and procedures were effective to ensure that information we are required to disclose in reports that we file or submit under the Exchange Act is recorded, processed, summarized and reported within the time periods specified in SEC rules and forms.

For this purpose, disclosure controls and procedures include controls and procedures designed to ensure that information that is required to be disclosed under the Exchange Act is accumulated and communicated to the Company's management, including the CEO and CFO, as appropriate, to allow timely decisions regarding required disclosure.

In light of the restatement discussed elsewhere in this 2014 Amended Annual Report on Form 10-K/A ("Form 10-K/A"), management, under the supervision and with the participation of our CEO and CFO, reevaluated the effectiveness of the Company's disclosure controls and procedures as of June 30, 2014 and concluded that the Company's disclosure controls and procedures were not effective due to the existence of the material weakness described in Management's Report on Internal Control over Financial Reporting (Revised).

Notwithstanding the material weakness identified by Company management, each of the Company's CEO and CFO has concluded, based on his knowledge, that the consolidated financial statements included in this Form 10-K/A fairly present in all material respects the Company's financial condition, results of operations and cash flows of the Company as of, and for the periods presented in this report, in conformity with accounting principles generally accepted in the United States.

The Management’s Report on Internal Control over Financial Reporting (Revised) 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, 2014; their report is included in Item 8 of this Form 10-K/A.

Changes in Internal Control over Financial Reporting

During the fiscal quarter ending June 30, 2014, there was 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.

Remediation

The Company has implemented a number of remediation steps to address the material weakness discussed above and to improve its internal controls.

With respect to the control deficiencies discussed in the Management's Report on Internal Control over Financial Reporting (Revised) the following steps have been initiated.

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| i. | Improve our risk assessment processes to identify inherent risks and complexities in accounting that could have financial reporting implications. |

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| ii. | Increase training and knowledge development for the individuals tasked with understanding various technical accounting matters associated with the Company's multiple element arrangement revenue recognition policies. Additionally, engage and retain experienced external advisors for technical assistance. |

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| iii. | Review and update our revenue recognition policies on a regular basis to incorporate changes in our business and accounting standards. |

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| iv. | Redesign of our contract review controls, focusing on key areas that may significantly impact revenue recognition. |

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| v. | Enhance the functionality of our systems and controls over reporting from the systems to account for bundled software arrangements properly. |

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| vi. | Develop improved internal audit programs and training for individuals tasked with monitoring our accounting for revenue recognition for multiple element software arrangements. |

The Company expects that the measures described above should remediate the material weakness identified and strengthen our internal control over financial reporting.

Management is committed to improving the Company's internal control processes.

As the Company continues to evaluate and improve its internal controls, additional measures to address the material weakness or modifications to certain of the remediation procedures described above may be

identified, which will be subject to audit procedures.

The Company expects to complete the required remedial actions during fiscal 2016.

PART IV

[removed: (a)] [added: (a)] The following documents are filed as part of this [removed: Report:][added: Report:]

[added: \-] Reports of Independent Registered Public Accounting Firm

[added: \-] Consolidated Statements of Income for the [removed: Years Ended] [added: years ended] June 30, [removed: 2011, 2010] [added: 2014 (Restated), 2013 (Restated)] and [removed: 2009][added: 2012 (Restated)]

[added: \-] Consolidated Balance Sheets as of June 30, [removed: 2011] [added: 2014 (Restated)] and [removed: 2010][added: 2013 (Restated)]

[added: \-] Consolidated Statements of Changes in Stockholders’ Equity for the [removed: Years Ended] [added: years ended] June 30, [removed: 2011, 2010] [added: 2014 (Restated), 2013 (Restated)] and [removed: 2009][added: 2012 (Restated)]

[added: \-] Consolidated Statements of Cash Flows for the [removed: Years Ended] [added: years ended] June 30, [removed: 2011, 2010] [added: 2014 (Restated), 2013 (Restated)] and [removed: 2009][added: 2012 (Restated)]

[added: \-] Notes to the Consolidated Financial Statements

Exhibit No. [added: Description]

[added: | 3.1.7 |] Restated Certificate of Incorporation, attached as Exhibit 3.1.7 to the Company’s Annual Report on Form 10-K for the Year ended June 30, 2003. [added: |]

[added: | 3.2.3 |] Restated and Amended Bylaws, attached as Exhibit [removed: 3.2.2] [added: 3.1] to the Company’s Current Report on Form 8-K filed [removed: November 13, 2008.][added: August 28, 2013. |]

[removed: The Company’s] [added: | 10.36 | Jack Henry & Associates, Inc.] 1995 Non-Qualified Stock Option Plan, [added: as amended May 9, 2008,] attached as Exhibit [removed: 10.3] [added: 10.36] to the Company’s Annual Report on Form 10-K [removed: for the Year Ended June 30, 1996.][added: filed August 29, 2008. |]

[added: | 10.8 |] Form of Indemnity Agreement which has been entered into as of August 27, 1996, between the Company and each of its Directors and Executive Officers, attached as Exhibit 10.8 to the Company’s Annual Report on Form 10-K for the Year Ended June 30, 1996. [added: |]

[removed: Amendment to the Company’s 1996] [added: | 10.32 | Form of Restricted] Stock [removed: Option Plan,] [added: Agreement (executives),] attached as Exhibit [removed: 10.1] [added: 10.32] to the Company’s Current Report on Form 8-K filed [removed: July 5, 2005.][added: September 10, 2007. |]

[removed: The Company’s] [added: | 10.39 | Revised Form of] Restricted Stock [removed: Plan,] [added: Agreement (executives),] attached as Exhibit [removed: 10.27] [added: 10.39] to the Company’s [removed: Annual] [added: Quarterly] Report on Form [removed: 10-K] [added: 10-Q] filed [removed: September 12, 2006.][added: November 6, 2009. |]

[removed: The Company’s] [added: | 10.38 | Jack Henry & Associates, Inc.] 2005 Non-Qualified Stock Option Plan, [added: as amended and restated May 9, 2008,] attached as Exhibit [removed: 10.28] [added: 10.38] to the Company’s Annual Report on Form 10-K filed [removed: September 12, 2006.][added: August 29, 2008. |]

[added: | 10.29 |] Jack Henry & Associates, Inc. 2006 Employee Stock Purchase Plan, attached as Exhibit 10.29 to the Company’s Current Report on Form 8-K filed November 6, 2006. [added: |]

[added: | 10.33 |] Form of [removed: Termination Benefits Agreement,] [added: Restricted Stock Agreement (Vice presidents and certain other managers),] attached as Exhibit [removed: 10.31] [added: 10.33] to the Company’s Current Report on Form 8-K filed September 10, 2007. [added: |]

[added: | 10.42 |] Form of Restricted Stock [removed: Agreement (executives),] [added: Unit Award Agreement,] attached as Exhibit [removed: 10.32] [added: 10.2] to the Company’s Current Report on Form 8-K filed [removed: September 10, 2007.][added: August 24, 2010. |]

[added: | 10.34 |] Amendment No. 2 to Jack Henry & Associates, Inc. 2006 Employee Stock Purchase Plan, attached as Exhibit 10.34 to the Company’s Current Report on Form 8-K filed November 1, 2007. [added: |]

[added: | 10.45 |] Jack Henry & Associates, Inc. [removed: 2007] [added: 2012] Annual Incentive Plan, [added: effective September 1, 2012 and approved by the stockholders on November 14, 2012,] attached as Exhibit [removed: 10.35] [added: 10.1] to the [removed: Company’s] [added: Company's] Current Report on Form 8-K filed November [removed: 1, 2007.][added: 16, 2012. |]

[added: | 10.46 |] Jack Henry & Associates, Inc. [removed: 1995] [added: 2005] Non-Qualified Stock Option Plan, as amended [removed: May 9, 2008,] [added: August 20, 2010,] attached as Exhibit [removed: 10.36] [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: August 29, 2008.][added: February 7, 2012. |]

[added: | 10.43 |] Jack Henry & [removed: Associates,] [added: Associates] Inc. [removed: 1996] [added: Restricted] Stock [removed: Option] Plan, as amended [removed: May] [added: and restated effective November] 9, [removed: 2008,] [added: 2010,] attached as Exhibit [removed: 10.37] [added: 10.1] to the Company’s [removed: Annual] [added: Current] Report on Form [removed: 10-K] [added: 8-K] filed [removed: August 29, 2008.][added: November 12, 2010. |]

[removed: Revised] [added: | 10.47 |] Form of Restricted Stock Agreement [removed: (executives),] [added: (independent directors),] attached as Exhibit [removed: 10.39] [added: 10.47] to the Company’s Quarterly Report on Form 10-Q filed November [removed: 6, 2009.][added: 8, 2013. |]

[added: | 10.40 |] Amended and Restated Credit Agreement among Jack Henry & Associates, Inc., Wells Fargo Bank, National Association, Bank of America, N.A., regions Bank and U.S. Bank National Association, attached as Exhibit 10.1 to the Company’s Current Report on Form 8-K filed June 9, 2010. [added: |]

[removed: Amendment to] [added: | 10.44 | Form of Performance Shares Agreement Under the] Jack Henry & [removed: Associates] [added: Associates,] Inc. Restricted Stock [removed: Plan dated August 20, 2010,] [added: Plan,] 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: September 12, 2012. |]

[added: | 21.1* |] List of the Company’s subsidiaries. [added: |]

[added: | 23.1 |] Consent of Independent Registered Public Accounting Firm. [added: |]

[added: | 31.1 |] Certification of [added: the] Chief Executive Officer. [added: |]

[added: | 31.2 |] Certification of [added: the] Chief Financial Officer. [added: |]

[added: | 32.1 |] Written Statement of the Chief Executive Officer Pursuant to 18 U.S.C. Section 1350. [added: |]

[added: | 32.2 |] Written Statement of the Chief Financial Officer Pursuant to 18 U.S.C. Section 1350. [added: |]

[added: | 101.INS |] XBRL Instance Document [added: |]

[added: | 101.SCH |] XBRL Taxonomy Extension Schema Document [added: |]

[added: | 101.CAL |] XBRL Taxonomy Extension Calculation Linkbase Document [added: |]

[added: | 101.DEF |] XBRL Taxonomy Extension Definition Linkbase Document [added: |]

[added: | 101.LAB |] XBRL Taxonomy Extension Label Linkbase Document [added: |]

[added: | 101.PRE |] XBRL Taxonomy Extension Presentation Linkbase Document [added: |]

[removed: *] Furnished with this [removed: Amendment No. 1 to] [added: report on] Form [removed: 10-K] [added: 10-K/A] are the following documents formatted in XBRL (Extensible Business Reporting Language): (i) the Consolidated Balance Sheets at June 30, [removed: 2011] [added: 2014] and June 30, [removed: 2010,] [added: 2013,] (ii) the Consolidated Statements of Income for the years ended June 30, [removed: 2011, 2010] [added: 2014, 2013] and [removed: 2009,] [added: 2012,] (iii) the Consolidated Statements of [added: Shareholders’ Equity for the years ended June 30, 2014, 2013 and 2012, (iv) the Consolidated Statements of] Cash Flows for the years ended June 30, [removed: 2011, 2010] [added: 2014, 2013] and [removed: 2009,] [added: 2012,] and [removed: (iv)] [added: (v)] Notes to Consolidated Financial Statements.

[added: *] Previously [removed: furnished as an exhibit to] [added: filed with] the Jack Henry & Associates, Inc. Annual Report on Form 10-K for the year ended June 30, [removed: 2011.][added: 2014, originally filed August 27, 2014.]

Pursuant to the requirements of Section 13 or 15(d) of the Securities Exchange Act of 1934, the registrant has duly caused this [removed: Amendment No. 1 to the Jack Henry & Associates, Inc. Annual Report on Form 10-K] [added: report] to be signed on its behalf by the undersigned, thereunto duly authorized this [removed: 1st] [added: 25th] day of [removed: September, 2011.][added: June, 2015.]

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| 10.48 | Form of Termination Benefits Agreements (executives), attached as Exhibit 10.48 to the Company’s Quarterly Report on Form 10-Q filed February 6, 2014. |

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\-

\-

\-

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Description

3.1.7

3.2.2

10.3

10.8

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

10.27

10.28

10.29

10.31

10.32

10.33

Form of Restricted Stock Agreement (Vice presidents and certain other managers), attached as Exhibit 10.33 to the Company’s Current Report on Form 8-K filed September 10, 2007.

10.34

10.35

10.36

10.37

10.38

Jack Henry & Associates, Inc. 2005 Non-Qualified Stock Option Plan, as amended and restated May 9, 2008, attached as Exhibit 10.38 to the Company’s Annual Report on Form 10-K filed August 29, 2008.

10.39

10.40

10.41

10.42

Form of Restricted Stock Unit Award Agreement, attached as Exhibit 10.2 to the Company’s Current Report on Form 8-K filed August 24, 2010.

10.43

Jack Henry & Associates Inc. Restricted Stock Plan, as amended and restated effective November 9, 2010, attached as Exhibit 10.1 to the Company’s Current Report on Form 8-K filed November 12, 2010.

21.1

23.1

31.1

31.2

32.1

32.2