UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

Washington, D.C. 20549

FORM 10-Q/A

Amendment No. 1

(Mark One)

OR

COMMISSION FILE NO. 001-34490

SYNTROLEUM CORPORATION

(Exact name of registrant as specified in its charter)

5416 S. Yale Suite 400

Tulsa, Oklahoma 74135

(Address of principal executive offices) (Zip Code)

Registrant’s telephone number, including area code: (918) 592-7900

Not Applicable

(Former name, former address and former fiscal year, if changed since last report)

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 website, 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 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 “small 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 of the Exchange Act).    Yes  ¨    No  x

At May 1, 2013, the number of outstanding shares of the issuer’s common stock was 9,932,088.

EXPLANATORY NOTE

The Company’s Quarterly Report on Form 10-Q, filed with the Securities and Exchange Commission on May 3, 2013, is being amended to correct the number of shares of common stock outstanding on May 1, 2013, as shown on its cover page. The incorrect number was supplied to the Company by its stock transfer agent, and the cover page as now amended sets forth the correct number. All other stock information contained in the filed Form 10-Q was and remains correct and no change is being made in any Item of the filed Form 10-Q other than the cover page.

This Form 10-Q/A should be read in conjunction with the filed Form 10-Q. Except as specifically noted above, this Form 10-Q/A does not modify or update disclosures in the filed Form 10-Q or otherwise reflect events occurring after the filing of the filed Form 10-Q.

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.

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INDEX TO EXHIBITS

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