UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

WASHINGTON, D.C. 20549

FORM 10-Q/A

Amendment No. 1

For the quarterly period ended September 30, 2011

Commission file number: 001-34734

ROADRUNNER TRANSPORTATION SYSTEMS, INC.

(Exact name of registrant as specified in its charter)

4900 S. PENNSYLVANIA AVE.

CUDAHY, WISCONSIN 53110

(Address of principal executive offices) (Zip code)

(414) 615-1500

(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.    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 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. (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

Number of shares of common stock, $0.01 par value, of registrant outstanding at November 09, 2011: 30,705,050.

EXPLANATORY NOTE

This Amendment No. 1 on Form 10-Q/A (this “Amendment No. 1”) amends the quarterly report on Form 10-Q of Roadrunner Transportation Systems, Inc. (the “Company”) for the quarterly period ended September 30, 2011 (the “Original Report”), filed with the Securities and Exchange Commission on November 14, 2011. This Amendment No. 1 is being filed to include Item 2 of Part II of Form 10-Q to provide information concerning equity securities of the Company sold by the Company during the quarterly period ended September 30, 2011 that were not registered under the Securities Act of 1933.

Other than the foregoing and the recently-dated certifications of the Company, as required by Rule 12b-15 under the Securities Exchange Act of 1934, no other changes have been made to the Company’s Original Report. This Amendment No. 1 continues to speak as of the period ending date in the Original Report of the Form 10-Q and does not reflect events occurring after the filing of the Original Report.

PART II—OTHER INFORMATION

On August 31, 2011, upon the closing of our acquisition of Prime Logistics Corporation (referred to as Prime), we issued 208,913 shares of our common stock to one of the former stockholders of Prime as partial consideration ($3.0 million) for the acquisition of Prime. We issued the shares of common stock in reliance upon Section 4(2) of the Securities Act of 1933, as amended, as a transaction by an issuer not involving a public offering.

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.