Exhibit 99.1 SECOND AMENDMENT AGREEMENT SECOND AMENDMENT AGREEMENT(this“Agreement”) dated as of September 24, 2003 by and between Scientific Learning Corporation (the“Borrower”) and Fleet National Bank (the“Bank”), amending a certain Revolving Loan Agreement dated as of March 9, 2001 between the Borrower and the Bank, as amended by that certain First Amendment Agreement dated as of March 26, 2002 (as amended, the“Loan Agreement”). W I T N E S S E T H WHEREAS,pursuant to the terms of the Loan Agreement, the Bank has made and continues to make revolving loans to the Borrower; and WHEREAS,the Borrower has requested that the Bank amend certain terms and conditions of the Loan Agreement in connection with the reduction of the Commitment under the Loan Agreement; and WHEREAS,the Bank is willing to amend certain terms and conditions of the Loan Agreement in connection with the reduction of the Commitment under the Loan Agreement on the terms and conditions set forth herein. NOW,THEREFORE, for good and valuable consideration, the receipt and sufficiency of which are hereby acknowledged, the parties hereto hereby agree as follows: §1. Definitions.Capitalized terms used herein without definition that are defined in the Loan Agreement shall have the same meanings herein as therein. §2. Ratification of Existing Agreements.All of the Borrower’s obligations and liabilities to the Bank as evidenced by or otherwise arising under the Loan Agreement, the Note and the other Loan Documents, except as otherwise expressly modified in this Agreement upon the terms set forth herein, are, by the Borrower’s execution of this Agreement, ratified and confirmed in all respects. In addition, by the Borrower’s execution of this Agreement, the Borrower represents and warrants that no counterclaim, right of set-off or defense of any kind exists or is outstanding with respect to such obligations and liabilities. §3. Representations and Warranties.The Borrower hereby represents and warrants to the Bank that all of the representations and warranties made by the Borrower in the Loan Agreement, the Note and the other Loan Documents are true and correct on the date hereof as if made on and as of the date hereof, except to the extent that any of such representations and warranties expressly relate by their terms to a prior date and for matters previously disclosed to the Bank in writing. §4. Conditions Precedent.The effectiveness of the amendment contemplated hereby shall be subject to the satisfaction on or before the date hereof of each of the following conditions precedent:
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