Exhibit 10.1

AMENDMENT NO. 1

TO

EMPLOYMENT AGREEMENT

This Amendment is made effective as of this 31st day of December, 2012, by and
between Cardiovascular Systems, Inc. (“CSI”) and David L. Martin (“Executive”).

WHEREAS, CSI and Executive entered into an Employment Agreement dated effective
December 19, 2006, (the “Agreement”), which provides for severance if
Executive’s employment is terminated by CSI without Cause or by Executive for
Good Reason; and

WHEREAS, it has come to CSI’s attention that certain provisions of the Agreement
should be clarified for compliance with Section 409A of the Internal Revenue
Code of 1986, as amended, and the notices, regulations and other guidance of
general applicability issued thereunder (“Code Section 409A), and the parties
desire to amend the Agreement for compliance with Code Section 409A in
accordance with Notice 2010-80.

NOW, THEREFORE, the parties agree as follows:

1. The first paragraph of Section 3.4 of the Agreement is hereby amended in its
entirety to read as follows:

“Severance. If Executive is terminated by CSI without Cause (as defined below),
or Executive terminates his employment for Good Reason (as defined below), and
Executive executes, returns and does not rescind, and all rescission periods
have expired, by the 60th day after the termination of Executive’s employment, a
release of claims agreement in a form supplied by CSI, then CSI shall: (i) pay
Executive at regular payroll intervals, beginning on the next regularly
scheduled payday coinciding with or immediately following the 60th day after the
termination of the Executive’s employment (subject to the application of Code
Section 409A as set forth in Section 3.5 below), an amount equal to twelve
(12) months of Executive’s then current base salary; and (ii) continue to pay
CSI’s ordinary share of premiums for twelve (12) calendar months for Executive’s
COBRA continuation coverage in CSI’s group medical, dental, and life insurance
plans (as applicable), provided Executive timely elects such continuation
coverage and timely pays Executive’s share of such premiums, if any.”

2. A new Section 3.5 of the Agreement is hereby added to read as follows:

“IRC Section 409A. This Agreement is intended to comply with Internal Revenue
Code Section 409A (‘Code Section 409A’) or an exemption thereunder and shall be
construed and administered in accordance with Code Section 409A. Any payments to
be made under this Agreement upon a termination of employment shall only be made
if such termination of employment constitutes a ‘separation from service’ under
Code Section 409A. Notwithstanding any other provision of this Agreement to the
contrary, if any of the payments described in this Agreement are subject to the
requirements of Code Section 409A and CSI determines that Executive is a
“specified employee” as defined in Code Section 409A as of the date of
Executive’s termination of employment, all or a portion of such payments will
not be paid or commence until the first payroll date that occurs after the
six-month anniversary of the date of Executive’s termination of employment, or,
if earlier, the

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date of Executive’s death, but only to the extent such delay is required for
compliance with Code Section 409A. Further, notwithstanding anything in this
Agreement to the contrary, CSI expressly reserves the right to amend this
Agreement without Executive’s consent to the extent necessary to comply with
Code Section 409A, as it may be amended from time to time, and the regulations,
notices and other guidance of general applicability issued thereunder.”

3. Except as set forth herein, all provisions of the Agreement shall remain in
full force and effect without modification. Further, nothing in this Amendment
is intended to modify the amount, timing or form of payment for the deferred
compensation benefits described in the Agreement, and this Amendment shall, at
all times, be construed in compliance with Code Section 409A.

4. Capitalized terms used in this Amendment, but not otherwise defined, shall
have the meanings assigned to them under the Agreement.

[Signature Page Follows]

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IN WITNESS WHEREOF, the parties hereto have caused this Amendment to be executed
on the day and year first above written.

 

CARDIOVASCULAR SYSTEMS, INC. By:   /s/ Laurence L. Betterley   Its: Chief
Financial Officer

/s/ David L. Martin

David L. Martin