United States

SECURITIES AND EXCHANGE COMMISSION

Washington, DC 20549

Form 10-K/A

Amendment No. 1

(Mark one)

For the fiscal year ended September 30, 2014

or

For the transition period from                      to                     .

Commission file No. 001-33322

CMS BANCORP, INC.

(Exact name of registrant as specified in its charter)

(914) 422-2700

(Registrant’s telephone number, including area code)

Securities registered pursuant to Section 12(b) of the Act:

Securities registered pursuant to section 12(g) of the Act:

None.

(Title of Class)

Indicate by check mark if the registrant is a well-known seasoned issuer, as defined in Rule 405 of the Securities Act.    Yes  ¨    No  x

Indicate by check mark if the registrant is not required to file reports pursuant to Section 13 or Section 15(d) of the Act.    Yes  ¨    No  x

Indicate by checkmark whether the registrant (1) has filed all reports required to be filed by Section 13 or 15(d) of the Securities Exchange Act of 1934 during the preceding 12 months (or for such shorter period that the registrant was required to file such reports), and (2) has been subject to such filing requirements for the past 90 days.    Yes  x    No  ¨

Indicate by check mark whether the registrant has submitted electronically and posted on its corporate Web site, if any, every Interactive Data File required to be submitted and posted pursuant to Rule 405 of Regulation S-T (§ 232.405 of this chapter) during the preceding 12 months (or for such shorter period that the registrant was required to submit and post such files).    Yes  x    No  ¨

Indicate by check mark if disclosure of delinquent filers pursuant to Item 405 of Regulation S-K (§ 229.405 of this chapter) 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 10-K or any amendment to this Form 10-K.  ¨

Indicate by check mark whether the registrant is a large accelerated filer, an accelerated filer, a non-accelerated filer, or a smaller reporting company. See the definitions of “large accelerated filer,” “accelerated filer” and “smaller reporting company” in Rule 12b-2 of the Exchange Act.

Indicate by check mark whether the registrant is a shell company (as defined in Rule 12b-2 of the Securities Exchange Act).    Yes  ¨    No  x

The aggregate market value of the voting and non-voting common equity held by non-affiliates of the registrant, computed by reference to the average bid and asked prices of the common stock as of March 31, 2014 was $10.3 million.

As of December 19, 2014, the registrant had 1,862,803 shares of common stock, par value $0.01 per share, outstanding.

EXPLANATORY NOTE

This Amendment No. 1 on Form 10-K/A (this “Amended Filing”) to CMS Bancorp, Inc.’s (“CMS Bancorp”) Annual Report on Form 10-K for the fiscal year ended September 30, 2014, initially filed with the U.S. Securities and Exchange Commission (“SEC”) on December 22, 2014 (“Original Filing”), is being filed in order to amend Item 9A, “Controls and Procedures,” of the Original Filing in response to comments received from CMS Bancorp’s independent auditor, BDO USA, LLP (“BDO”) by letter dated January 12, 2015. In addition, this Amended Filing also includes an updated reference to the Company’s bylaws in Exhibit 3.4 and updated certifications from our Chief Executive Officer and Chief Financial Officer, as required by Sections 302 and 906 of the Sarbanes-Oxley Act of 2002 and the rules of the SEC, including Rule 12b-15.

Except as set forth herein, this Amendment No. 1 to Form 10-K continues to speak as of the date of the Original Filing and does not modify, amend or update in any way the financial statements or any other item or disclosures in the Original Filing. This Amended Filing does not reflect events occurring after the filing of the Original Filing or modify or update those disclosures that may be affected by subsequent events. Such subsequent matters will be addressed in subsequent reports filed with the SEC. Accordingly, this Amended Filing should be read in conjunction with the Original Filing and our other filings with the SEC.

ITEM 9A. CONTROLS AND PROCEDURES

Management’s Report on Internal Control over Financial Reporting

Management is responsible for establishing and maintaining adequate internal control over financial reporting for CMS Bancorp. CMS Bancorp’s internal control over financial reporting is a process designed under the supervision of its President and Chief Executive Officer (“CEO”) and Senior Vice President and Chief Financial Officer (“CFO”) to provide reasonable assurance regarding the reliability of financial reporting and the preparation of our financial statements for external purposes in accordance with U.S. generally accepted accounting principles.

Because of its inherent limitations, internal control over financial reporting may not prevent or detect misstatements. Also, projections of any evaluation of effectiveness to future periods are subject to the risk that controls may become inadequate because of changes in conditions, or that the degree of compliance with the policies or procedures may deteriorate.

On January 13, 2015, the Management and Audit Committee of CMS Bancorp’s Board of Directors received a letter dated January 12, 2015 from CMS Bancorp’s independent accounting firm, BDO USA, LLP (“BDO”), which letter concluded that CMS Bancorp had a material weakness in its internal control over financial reporting related to an audit adjustment of $101,000 in connection with unaccrued legal fees at September 30, 2014. The unaccrued fees were identified after September 30, 2014 based on bills submitted by CMS Bancorp’s outside legal counsel to CMS Bancorp in the fourth calendar quarter of 2014.

CMS Bancorp attributed the material weakness in part to the sudden and unexpected death of CMS Bancorp’s former Chief Financial Officer in August 2014, which management concluded and BDO agreed was an event that led to a “loss of institutional knowledge” that was a “significant obstacle to overcome.” CMS Bancorp recorded the aforementioned $101,000 adjustment and such adjustment was reflected in our financial statements contained in the Annual Report on Form 10-K for the fiscal year ended September 30, 2014, which we filed with the SEC on December 22, 2014.

Management has made a comprehensive review, evaluation, and assessment of CMS Bancorp’s internal control over financial reporting as of September 30, 2014. In making its assessment of internal control over financial reporting, management used the criteria issued by the Committee of Sponsoring Organizations of the Treadway Commission in Internal Control-Integrated Framework (1992). Based on that assessment, and in light of the material weakness finding by BDO, management concluded that, as of September 30, 2014, CMS Bancorp’s internal control over financial reporting was not effective based on the criteria. However, management has implemented enhancements to its internal controls to ensure that the material weakness has been fully remediated. Specifically, the Company hired a new CFO in October 2014 and is working with the new CFO to implement review and reporting processes to enhance our controls over analyzing and recording appropriate adjustments to accrued expenses so that they operate in an effective manner.

This Annual Report on Form 10-K does not include an attestation report of CMS Bancorp’s independent registered public accounting firm regarding internal control over financial reporting. Management’s report was not subject to attestation by CMS Bancorp’s registered public accounting firm pursuant to rules of the SEC applicable to smaller reporting companies.

Changes in Internal Control over Financial Reporting

There were no changes in CMS Bancorp’s internal control over financial reporting identified in connection with the evaluation that occurred during CMS Bancorp’s last fiscal quarter that ended on September 30, 2014. As noted above, the sudden and unexpected death of CMS Bancorp’s former Chief Financial Officer in August 2014 was an event that led to a “loss of institutional knowledge” that was a “significant obstacle to overcome,” which contributed to the material weakness finding by BDO. Subsequent to the end of the last fiscal quarter, CMS Bancorp hired a new Chief Financial Officer in October 2014 and implemented enhancements to its internal controls to ensure that the material weakness has been fully remediated.

Evaluation of Disclosure Controls and Procedures

Management has conducted an evaluation, with the participation of CMS Bancorp’s CEO and CFO, of the effectiveness of CMS Bancorp’s disclosure controls and procedures (as defined in Exchange Act Rules 13a-15(e) and 15d-15(e)) as of the end of the period covered by this report and after the Original Filing on December 22, 2014. Based upon that evaluation, CMS Bancorp’s CEO and CFO concluded that the disclosure controls and procedures were not effective as of September 30, 2014 due to the material weakness in our internal control over financial reporting as described above. As noted above, management has implemented enhancements to its internal controls to ensure that the material weakness has been fully remediated.

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Exhibit Index

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SIGNATURES

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.

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