AMENDMENT AND CONSENT AGREEMENT

Exhibit 10.1

AMENDMENT AND CONSENT AGREEMENT

This Amendment and Consent Agreement (this “Agreement”) is made as of January 29, 2013, by and among Aegerion Pharmaceuticals, Inc., a Delaware corporation (the “Company”), and certain holders of the Company’s outstanding common stock, $0.001 par value per share, issued in connection with the conversion of the Company’s Series A Convertible Preferred Stock, $0.001 par value per share (the “Series A”), and Series B Convertible Preferred Stock, $0.001 par value per share (the “Series B” and together with the Series A, the “Preferred Stock”).

Reference is hereby made to that certain Amended and Restated Investor Rights Agreement dated as of November 9, 2007, by and among the Company and the investors listed on Schedule I attached thereto (the “Investors”), as amended and in effect from time to time (the “Investor Rights Agreement”).

WHEREAS, Section 6.4 of the Investor Rights Agreement provides, among other things, that the Investor Rights Agreement may not be amended or modified, and no provision thereof may be waived, without the written consent of the Company and the holders of at least two-thirds of the Preferred Stock (the “Required Supermajority”); and

WHEREAS, the Company and the Investors representing the Required Supermajority agree that the amendment set forth below.

NOW, THEREFORE, the Company and the undersigned Investors, constituting the Required Supermajority, on behalf of all Investors, hereby consent to the following:

“6.16 Termination. Notwithstanding anything to the contrary contained herein, this Investor Rights Agreement shall terminate in its entirety, and be of no further force or effect, on February 1, 2013.”

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IN WITNESS WHEREOF, the undersigned have duly executed this Agreement as of the date first written above.

COMPANY:

INVESTORS:

[Signature Page to Amendment and Consent Agreement]

[Signature Page to Amendment and Consent Agreement]