Exhibit 10.1

AMENDMENT TO THE AMENDED AND RESTATED SAREPTA THERAPEUTICS, INC. 2011 EQUITY
INCENTIVE PLAN

AMENDMENT NO. 1

TO THE

SAREPTA THERAPEUTICS, INC.

AMENDED AND RESTATED 2011 INCENTIVE PLAN

WHEREAS, the Board of Directors (the “Board”) of Sarepta Therapeutics, Inc. (the
“Company”) and the stockholders of the Company (the “Shareholders”) previously
adopted and approved the Sarepta Therapeutics, Inc. 2011 Amended and Restated
Equity Incentive Plan (as amended and/or restated, the “Plan”); and

WHEREAS, the Board has determined that it is in the best interests of the
Company to amend the Plan, subject to approval by the Shareholders, to increase
the number of authorized shares under the Plan by 1,700,000 shares of common
stock of the Company is authorized under the Plan;

NOW, THEREFORE, the Plan hereby is amended, effective on the date of approval by
the Board, as follows:

1. The first sentence of Section 3(a) of the Plan, entitled “Stock Subject to
the Plan,” shall be replaced in its entirety by the following:

“Subject to adjustment pursuant to Section 15(a) of the Plan, the maximum
aggregate number of Shares that may be subject to Awards and sold under the Plan
is 6,236,903 Shares, plus the number of shares subject to outstanding awards
under the 2002 Equity Incentive Plan (the “2002 Plan”) that expire or otherwise
terminate without having been exercised in full, or are forfeited to or
repurchased by us, up to a maximum of 514,161 shares; provided, however, that
such aggregate number of Shares available for issuance under the Plan shall be
reduced by 1.41 shares for each Share delivered in settlement of any Full Value
Award and, provided further, that no more than 5,000,000 shares may be issued
upon the exercise of Incentive Stock Options.”

2. Except as modified herein, the Plan is hereby specifically ratified and
affirmed.

This Amendment No. 1 to the Plan is adopted by the Board effective as of the
date of approval by shareholders at the 2015 Annual Meeting.