UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

WASHINGTON, D.C. 20549

FORM 10-Q/A

Amendment No. 1

For the quarterly period ended September 30, 2013

OR

For the transition period from                      to                     

Commission File Number 000-31719

POZEN Inc.

(Exact name of registrant as specified in its charter)

1414 Raleigh Road

Suite 400

Chapel Hill, North Carolina 27517

(Address of principal executive offices, including zip code)

(919) 913-1030

(Registrant’s telephone number, including area code)

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.    x  Yes    ¨  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).    x  Yes    ¨  No

Indicate by check mark whether the registrant is a large accelerated filer, an accelerated filer, or a non-accelerated filer. See definition of “accelerated filer” and “large accelerated filer” in Rule 12b-2 of the Securities Exchange Act of 1934. (Check one):

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

The number of shares outstanding of the registrant’s common stock as of October 24, 2013 was 30,507,451.

Explanatory Note

This Form 10-Q/A (“Amendment No. 1”) to POZEN, Inc.’s (the “Company”) Quarterly Report on Form 10-Q for the fiscal quarter ended September 30, 2013, initially filed with the Securities and Exchange Commission (the “SEC”) on November 6, 2013 (the “Original Filing”), is being filed as an exhibit-only filing in response to communications received from the SEC in connection with the confidential treatment request made with respect to Exhibit 10.2 (License and Collaboration Agreement between POZEN Inc. and sanofi-aventis U.S. LLC, dated as of September 3, 2013). Item 6 of Part II of the Original filing is hereby amended to include a revised redacted version of Exhibit 10.2.

The Original Filing has not been updated other than for the change to Part II, Item 6 indicated above. No other items included in the Form 10-Q have been amended, and such items remain in effect as of the filing date of the Form 10-Q. This Amendment No. 1 does not purport to provide an update or a discussion of any developments at the Company subsequent to the original filing date of the Original Filing.

In addition, as required by Rule 12b-15 under the Securities Exchange Act of 1934, as amended, new certifications by our principal executive officer and principal financial officer are filed herewith as exhibits to this Amendment No. 1.

Item 6. Exhibits

SIGNATURES

Pursuant to the requirements 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.