UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

Washington, D.C. 20549

Form 10-K/A

(Amendment No. 1)

ANNUAL REPORT UNDER SECTION 13 or 15(d)

OF THE SECURITIES EXCHANGE ACT OF 1934

(Mark One)

For the Fiscal Year Ended December 31, 2005

or

For the transition period from             to             

Commission File Number: 000-29959

Pain Therapeutics, Inc.

(Exact name of registrant as specified in its charter)

7801 N. Capital of Texas Highway, Suite 260, Austin, TX 78731

(512) 501-2444

(Address, including zip code, or registrant’s principal executive offices and telephone number, including area code)

416 Browning Way, South San Francisco, CA 94080

(former address)

Securities registered pursuant to Section 12(b) of the Act: Common Stock, $0.001 par value

Securities registered pursuant to Section 12(g) of the Act: None

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 check mark 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.  x

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 definition of “large accelerated filer”, “accelerated filer” and “smaller reporting company” in Rule 12b-2 of the Exchange Act. (Check one):

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

The aggregate market value of the voting and non-voting common equity held by non-affiliates was $144,131,648 computed by reference to the last sales price of $3.87 as reported by the NASDAQ Global Select Market, as of the last business day of the Registrant’s most recently completed second fiscal quarter, June 30, 2011.

The number of shares outstanding of the Registrant’s common stock on April 17, 2012 was 44,732,017.

DOCUMENTS INCORPORATED BY REFERENCE

None.

FORM 10-K/A

INDEX

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EXPLANATORY NOTE

This Amendment No. 1 on Form 10-K/A (this “Amendment”) amends Pain Therapeutics, Inc.’s (the “Company”) Annual Report on Form 10-K for the year ended December 31, 2005, originally filed on February 24, 2006 (the “Original Filing”). The Company is re-filing Item 15 of Part IV to reflect expiration of confidential treatment of certain terms excluded from exhibits 10.8 and 10.9 to the Original Filing, and to re-file such exhibits to include the originally omitted portions that were subject to the now expired order for confidential treatment. In addition, pursuant to the rules of the Securities and Exchange Commission, the Company is including with this Amendment certain currently dated certifications.

Except as described above, and other than changes to update the form of cover page to this filing to conform to the format of the current cover page on the Annual Report on Form 10-K, as promulgated by the Securities and Exchange Commission, and certain information in the cover page, no other changes have been made to the Original Filing. The filing of this Form 10-K/A is not a representation that any statements contained in items of Form 10-K other than Part IV, Item 15 are true or complete as of any date subsequent to the Original Filing.

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PART IV

Item 15. Exhibits and Financial Statement Schedules

(a) The following documents are filed as part of this Form 10-K:

(1) Financial Statements (included in Part II of this report):

 Reports of Independent Registered Public Accounting Firm

 Balance Sheets

 Statements of Operations

 Statement of Stockholders’ Equity

 Statements of Cash Flows

 Notes to Financial Statements

(2) Financial Statement Schedules:

 All financial statement schedules are omitted because the information is inapplicable or presented in the notes to the financial  statements.

(3) Exhibits:

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(b) Exhibits

The exhibits listed under Item 14(a)(3) hereof are filed as part of this Form 10-K other than Exhibit 32.1, which shall be deemed, furnished.

(c) Financial Statement Schedules

All financial statement schedules are omitted because the information is inapplicable or presented in the notes to the financial statements.

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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 Form 10-K/A to be signed on its behalf by the undersigned, thereunto duly authorized.

Dated: May 9, 2012

Pursuant to the requirements of the Securities Exchange Act of 1934, this Form 10-K/A has been signed below by the following persons on behalf of the registrant and in the capacities and on the dates indicated.

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EXHIBIT INDEX

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