United States

SECURITIES AND EXCHANGE COMMISSION

Washington, DC 20549

Amendment No. 1 on Form 10-K

to Form 10-KSB

(Mark one)

For the fiscal year ended September 30, 2007

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 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 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.    x

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 issuer’s revenues for the fiscal year ended September 30, 2007 were $7.8 million.

The aggregate market value of the 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 December 11, 2007 was $18.3 million.

As of the latest practicable date, the registrant had 2,055,165 shares of common stock, par value $0.01 per share, outstanding.

EXPLANATORY NOTE:

This Amendment No. 1 (this “Amendment No. 1”) on Form 10-K to Form 10-KSB for the fiscal year ended September 30, 2007 is being filed to include the signature of the Chief Financial Officer (Principal Financial and Accounting Officer), which was inadvertently omitted from the signature page to the Form 10-KSB filed on December 28, 2007. This Amendment No. 1 is also being filed to identify the Principal Executive Officer, whose identification was inadvertently omitted from the signature page.

We are also including in this Amendment No. 1 updated Exhibit Index references and certifications of our principal executive and principal financial officers. This Amendment No. 1 to our Annual Report on Form 10-KSB as originally filed on December 28, 2007 (the “Original Report”) continues to speak as of the date of our Original Report, and we have not updated the disclosures contained in this Amendment No. 1 to reflect any events that occurred subsequent to the filing of the Original Report.

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.

Pursuant to the requirements of the Securities Exchange Act of 1934, this report has been signed below by the following persons on behalf of the registrant and in the capacities and on the dates indicated.

SIGNATURES

Pursuant to the requirements of Section 13 or 15(d) of the Securities Exchange Act of 1934, the registrant has duly caused this Amendment No. 1 on Form 10-K to Form 10-KSB to be signed on its behalf by the undersigned, thereunto duly authorized.

EXHIBIT INDEX