Exhibit 99.2

THIRD AMENDMENT TO FACILITY AGREEMENT

THIRD AMENDMENT dated as of January 10 2012 (this “Amendment”) to the FACILITY AGREEMENT (the “Agreement”), dated as of June 17, 2009, as amended on August 5, 2010 and March 28, 2011, between Arena Pharmaceuticals, Inc., a Delaware corporation (the “Borrower”), and those lenders set forth on the signature page hereof (individually, a “Lender” and together, the “Lenders” and, collectively with the Borrower, the “Parties”).

WITNESSETH:

WHEREAS, on July 6, 2009, the Borrower borrowed from the Lenders $100,000,000 pursuant to the Agreement;

WHEREAS, on the date hereof the Borrower and the Lenders have entered into a Securities Purchase Agreement (the “SPA-2012”), pursuant to which the Lenders have agreed to purchase from the Borrower, and the Borrower has agreed to issue and sell to the Lenders, shares of the Borrower’s Common Stock and Preferred Stock; and

WHEREAS, the Borrower desires to prepay the Loan (as defined in the Agreement) in the aggregate amount of $5,000,000;

NOW, THEREFORE, in consideration of the mutual agreements set forth herein, the Lenders and the Borrower agree as follows:

1. Concurrently with the Closing (as defined in the SPA) the Borrower shall prepay the Loan in the amount of $5,000,000. Section 2.12(d) of the Agreement shall not apply to such prepayment.

2. Section 1.1 of the Agreement is amended to add a definition entitled “SPA-2012” to read as follows:

“SPA-2012” means that certain Securities Purchase Agreement, dated as of January 10, 2012, by and between Borrower and the Lenders.”

3. Section 5.2 of the Agreement is amended to add thereto a subsection (f) to read as follows:

“(f) The Borrower shall not, during the 30 day period following the closing of the SPA-2012, sell any Common Stock, Convertible Securities or options, other than in an Exempted Issuance.”

4. Except as amended by this Amendment, the Agreement remains in full force and effect.

IN WITNESS WHEREOF, the undersigned Lenders and the Borrower have caused this Amendment to be duly executed as of the date first written above.

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