UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

WASHINGTON, DC 20549

FORM 8-K

CURRENT REPORT

Pursuant to Section 13 or 15(d) of the

Securities Exchange Act of 1934

Date of Report (Date of earliest event reported): June 18, 2013

SANTARUS, INC.

(Exact Name of Registrant as Specified in Its Charter)

3611 Valley Centre Drive, Suite 400, San Diego, California 92130

(Address of Principal Executive Offices) (Zip Code)

(858) 314-5700

(Registrant’s Telephone Number, Including Area Code)

N/A

(Former Name or Former Address, if Changed Since Last Report)

Check the appropriate box below if the Form 8-K filing is intended to simultaneously satisfy the filing obligation of the registrant under any of the following provisions:

On June 18, 2013, Santarus, Inc. (“Santarus”) and Pharming Group NV (“Pharming”) announced that the U.S. Food and Drug Administration (“FDA”) has accepted for filing the Biologics License Application (“BLA”) for the investigational drug Ruconest^® (recombinant human C1 esterase inhibitor) 50 IU/kg. Santarus and Pharming are seeking U.S. marketing approval of Ruconest for the treatment of acute angioedema attacks in patients with hereditary angioedema (“HAE”). The FDA indicated that as part of its review it plans to present the BLA to the Blood Products Advisory Committee. Pursuant to the Prescription Drug User Fee Act (“PDUFA”) guidelines, Santarus and Pharming expect the FDA will complete its review or otherwise respond to the Ruconest BLA by April 16, 2014. A copy of the press release is attached hereto as Exhibit 99.1 and is incorporated herein by reference.

Forward-Looking Statements

Santarus cautions you that statements included in this report that are not a description of historical facts are forward-looking statements. The inclusion of forward-looking statements should not be regarded as a representation by Santarus that any of its plans or objectives will be achieved. Actual results may differ materially from those set forth in this report due to the risks and uncertainties inherent in Santarus’ business, including, without limitation: whether the FDA will approve the Ruconest BLA in a timely manner or at all; whether the FDA will concur with the clinical interpretation of the phase III study results or the conduct of the study; whether the FDA ultimately will require additional clinical studies or other development programs before approving Ruconest; risks related to Santarus’ dependence on Pharming for many functions related to Ruconest, and Pharming’s ability to continue to perform these functions based on its limited financial resources; risks related to the license and supply arrangements between Santarus and Pharming, including the potential for termination of the arrangements; other difficulties or delays in development, testing, manufacturing and marketing of, and obtaining and maintaining regulatory approvals for, Santarus’ products; and other risks detailed in Santarus’ prior public periodic filings with the Securities and Exchange Commission, including Santarus’ Quarterly Report on Form 10-Q for the quarter ended March 31, 2013.

You are cautioned not to place undue reliance on these forward-looking statements, which speak only as of the date hereof. All forward-looking statements are qualified in their entirety by this cautionary statement and Santarus undertakes no obligation to revise or update this report to reflect events or circumstances after the date hereof. This caution is made under the safe harbor provisions of Section 21E of the Private Securities Litigation Reform Act of 1995.

(d) Exhibits.

SIGNATURE

Pursuant to the requirements of the Securities Exchange Act of 1934, as amended, the Registrant has duly caused this report to be signed on its behalf by the undersigned hereunto duly authorized.

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