Karyopharm Therapeutics Inc. Annual Bonus Plan

Exhibit 10.1

KARYOPHARM THERAPEUTICS INC. ANNUAL BONUS PLAN

The Karyopharm Therapeutics Inc. (“Karyopharm” or the “Company”) Annual Bonus Plan (the “Plan”) has been established to attract, motivate, and retain employees by promoting and rewarding the achievement of key short-term corporate objectives as well as individual performance and to align the interests of employees and stockholders. Cash-based annual performance bonus awards (“Actual Bonus Awards”) may be granted and earned according to the Plan.

A Plan Year is defined as the calendar year from January 1 to December 31 (“Plan Year”), although the Plan’s terms will apply through the date Actual Bonus Awards for the applicable Plan Year are paid.

To be a participant for any applicable Plan Year, both Criteria #1 and Criteria #2, as defined below, must be met:

Each participant’s Actual Bonus Award shall be prorated based on the number months that the participant met Criteria #1. The number of months that a participant’s Bonus Award shall be prorated (“Months Eligible”) shall be determined by the following guidelines:

Examples to determine Months Eligible:

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For a participant to remain eligible to earn an Actual Bonus Award for a Plan Year, the participant must:

Other factors, as discussed in V. Impact of Participant Eligibility, may affect a Participant’s payout.

Each participant’s Target Bonus Percentage is determined by his or her grade as of December 31 of the applicable Plan Year.

A participant’s Target Bonus Award is calculated by multiplying the participant’s annual base salary on December 31 of the applicable Plan Year (“Annual Salary”), Target Bonus Percentage, and Months Eligible out of 12.

Target Bonus Award = Annual Salary x Target Bonus Percentage x (Months Eligible/12)

See VI. Example to Calculate Target and Actual Bonus Awards, below.

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Actual Bonus Awards can be allocated into two components, corporate and individual. The criteria upon which each of these components are measured are described below.

Corporate Component

On or before March 31 of a Plan Year, the Compensation Committee of the Company’s Board of Directors (the “Compensation Committee”) shall set corporate goals and weight each corporate goal according to its priority and anticipated impact on the Company.

Following the end of a Plan Year, the Compensation Committee has discretion to determine the Company’s overall actual corporate performance for that Plan Year as a cumulative percentage of goals achieved (“Corporate Performance”). Partial or excess achievement as compared to the original goal weighting may be determined for each goal, at the discretion of the Compensation Committee.

Individual Component

For each Plan Year, managers and executives of the Company (or in the case of executive officers of the Company, the Board of Directors or the Compensation Committee) shall determine each participant’s Individual Performance Goals (“Individual Goals”) and weight each goal according to its priority and anticipated impact on the Company.

Following the end of a Plan Year, the managers and executives of the Company (or in the case of executive officers of the Company, the Board of Directors or the Compensation Committee) have discretion to determine the participant’s actual individual performance percentage (“Individual Performance”) for that Plan Year as a cumulative percentage of Individual Goals. Partial or excess achievement as compared to the original goal weighting may be determined for each goal.

In addition to achievement of Individual Goals, as described above, to determine Individual Performance, managers and executives (or in the case of executive officers of the Company, the Board of Directors or the Compensation Committee) may also consider qualitative factors related to the Company’s core values and individual performance.

The weight of corporate and individual components in the calculation of Actual Bonus Award for each Participant will depend on his or her grade:

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If the Compensation Committee, in its sole discretion, determines that the cumulative percentage of goals achieved does not meet a minimum threshold for payout based on the corporate component, participants may be eligible to receive a payout based on their individual component.

Actual Bonus Awards for a participant will be calculated by multiplying a participant’s Target Bonus Award by the sum of the applicable Corporate and the participant’s Individual Performance (adjusted by each applicable weight).

Actual Bonus Award = Target Bonus Award x [(corporate weight x Corporate Performance) + (individual weight x Individual Performance)]

See VI. Example to Calculate Target and Actual Bonus Awards, below.

An example participant’s bonus inputs are below:

Target Bonus Award:

Target Bonus Award = Annual Salary x Target Bonus Percentage x (Months Eligible/12)

Actual Bonus Award:

Actual Bonus Award = Target Bonus Award x [(corporate weight x Corporate Performance) + (individual weight x Individual Performance)]

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As described above, a participant must remain employed with Karyopharm through the Payout Date in order to receive an Actual Bonus Award for a Plan Year. Therefore, if a participant’s employment terminates for any reason prior to the Payout Date, the participant will not be eligible for an Actual Bonus Award, with the following exception:

Participants who are promoted during a Plan Year to a grade with a higher Target Bonus Percentage and/ or different corporate and individual weighting are eligible for the Target Bonus Percentage and weightings for their grade in effect as of December 31^st of the Plan Year.

Participants who change grades resulting in a lower Target Bonus Percentage as of December 31 are eligible for a prorated Actual Bonus Award based on the number of months in the Plan Year they were employed in a grade at the higher target percentage plus a prorated Actual Bonus Award based on the number of months in the Plan Year they were employed at the lower Target Bonus Percentage.

Participants who have a change in their regularly scheduled hours, described above as Criteria #1, will be eligible for a prorated Actual Bonus Award based on the number of weeks that their regularly scheduled weekly hours were 30 hours/week or more.

Short-Term Disability, FMLA, and other state-specific family and medical leave acts. Participants will continue to be eligible for an Actual Bonus Award during the period of the leave of absence.

Long-Term Disability (“LTD”), including LTD combined with Workers’ Compensation. Participants who are on LTD in excess of Federal or State mandated family and medical leave provisions, will not be eligible for an Actual Bonus Award for the period of the LTD.

Personal Unpaid Leaves of Absence. Participants who are on a personal unpaid leave of absence, which is not covered by any of the above provisions, are not eligible for an Actual Bonus Award for the period of the personal leave of absence.

Participants who transfer in or out of a position eligible to receive an Actual Bonus Award under the Plan will be eligible for a pro-rated portion of the participant’s Actual Bonus Award based on the number of months they qualified for participation under the Plan during the applicable Plan Year.

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The Payout Date for Actual Bonus Awards is made in the calendar year following the applicable Plan Year, on or before March 15^th of such following calendar year, to all participants who remain eligible as of the Payout Date, including those on any type of leave of absence and those whose employment has previously terminated on account of death but who are eligible for an Actual Bonus Award per the terms of the Plan.

The Board of Directors may terminate, suspend or modify (and if suspended, may reinstate with or without modification) all or part of the Plan at any time, with or without notice to participants. The Compensation Committee has sole authority to administer or interpret the Plan, and the Compensation Committee retains its right to exercise discretion as it sees fit. Notwithstanding anything herein to the contrary, the Board of Directors may determine that no Actual Bonus Awards shall be paid hereunder for a particular Plan Year or to a particular participant or participants, notwithstanding the level of achievement of Corporate and/ or Individual Performance for such Plan Year.

The Compensation Committee reserves the exclusive right to determine eligibility to participate in this Plan and to interpret all applicable terms and conditions, including eligibility criteria, performance objectives and payment conditions, for the Company’s executive officers. The Compensation Committee delegates to each of the Company’s Chief Executive Officer, President, highest human resources officer and highest finance officer the authority to administer, and determine eligibility to participate in, the Plan and interpret all applicable terms and conditions for employees who are not executive officers of the Company. The determinations and interpretations of the Compensation Committee and its delegates will be conclusive.

All Actual Bonus Awards are paid from the Company’s general assets. No trust, account or other separate collection of amounts will be established for the payment of Actual Bonus Awards under the Plan. Actual Bonus Awards are unfunded obligations of the Company, so if and when an Actual Bonus Award becomes due, a participant’s rights to payment are no greater than the rights of a general unsecured creditor.

Section 409A It is intended that this Plan comply with or be exempt from Section 409A of the Internal Revenue Code of 1986 (the “Code”), and the Treasury Regulations and IRS guidance thereunder (collectively referred to as “Section 409A”), and notwithstanding anything to the contrary herein, it shall be administered, interpreted, and construed in a manner consistent with Section 409A. If and to the extent required to comply with Section 409A, no payment or benefit required to be paid under this Plan on account of termination of a participant’s employment shall be made unless and until the participant incurs a “separation from service” within the meaning of Section 409A. If and to the extent any portion of any payment, compensation or other benefit provided to a participant in connection with the participant’s employment termination is determined to constitute “nonqualified deferred compensation” within the meaning of Section 409A of the Code, and the participant is a specified employee as defined in Section 409A(a)(2)(B)(i) of the Code, as determined by the Company in accordance with its procedures, by which determination participants hereby agree to be bound, such portion of the payment, compensation or other benefit shall not be paid before the earlier of (i) the expiration of the six month period measured from the date of the participant’s “separation from service” (as determined under Section 409A of the Code) or (ii) the tenth day following the date of the participant’s death following such separation from service (the “New Payment Date”). The aggregate of any payments that otherwise would have been paid to the participant during the period between the date of separation from service and the New Payment Date shall be paid in a lump sum in the first payroll period beginning after such New Payment Date. Notwithstanding anything herein to the contrary, the Company shall have no liability to any Plan participant or to any other person in the event that the payments that may be earned hereunder do not comply with or are not exempt from Section 409A.

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Withholding. The Company shall withhold from any Actual Bonus Award any federal, state and local income, employment, other similar taxes, or 401(k) deferrals as may be required to be withheld pursuant to any applicable law, regulation, or Company 401(k) policy.

At-Will Employment. This document sets forth the terms of the Plan and is not intended to be a contract or employment agreement between you or any other participant and the Company. Nothing in this Plan shall alter the at-will nature of your employment. You are free to resign at any time, and for any or no reason. Similarly, the Company is free to terminate its employment relationship with you at any time, with or without cause.

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