UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

Washington, D.C. 20549

Form 10-Q/A

Amendment No. 2

For the quarterly period ended March 31, 2011

Commission File Number: 001-33151

HANSEN MEDICAL, INC.

(Exact name of registrant as specified in its charter)

800 East Middlefield Road, Mountain View, CA 94043

(Address of Principal Executive Offices)

(650) 404-5800

(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  þ    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 during the preceding 12 months (or for such shorter period that the registrant was required to submit and post such files).    Yes  ¨    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 definition of “large accelerated filer,” “accelerated filer” and “smaller reporting company” in Rule 12b-2 of the Exchange Act.

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

The number of shares outstanding of the registrant’s common stock as of April 29, 2011 was 54,547,487.

EXPLANATORY NOTE

Hansen Medical, Inc. (the “Company”) filed its Quarterly Report on Form 10-Q for the quarter ended March 31, 2011 with the Securities and Exchange Commission on May 10, 2011 (the “Form 10-Q”), as amended by Amendment No. 1 to its Quarterly Report on Form 10-Q/A filed with the Securities and Exchange Commission on June 1, 2011 (“Amendment No. 1”). This Form 10-Q/A Amendment No. 2 (“Amendment No. 2”) is being filed to amend the aforementioned Quarterly Report on Form 10-Q as an exhibit-only filing in response to comments received from the staff of the Securities and Exchange Commission regarding a request for confidential treatment of certain portions of Exhibits 10.68, 10.69, 10.70 and 10.72 originally filed with the Form 10-Q. This Amendment No. 2 amends and restates the exhibit index included in Part II, Item 6 of the Form 10-Q.

The Form 10-Q, as amended by Amendment No. 1, 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, as amended by Amendment No. 1, have been amended, and such items remain in effect as of the respective filing dates of the Form 10-Q and Amendment No. 1. This Amendment No. 2 does not purport to provide an update or a discussion of any developments at the Company subsequent to the original filing date of the Form 10-Q.

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. 2.

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PART II — OTHER INFORMATION

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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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