Under the Office of the President, the administration of CSU San Marcos is comprised of five divisions:
- Academic Affairs
- Student Affairs
- Finance & Administrative Services
- University Advancement
- Community Engagement
In addition, the newly-formed Office of University Ombuds provides confidential, neutral, and informal dispute resolution services for all faculty, staff members and students.
The University also has a long-standing cooperative relationship with the following non-profit auxiliaries:
- University Auxiliary and Research Services Corporation (UARSC)
Oversees campus amenities such as food service and bookstores
- Associated Students, Inc. (ASI)
Student-run auxiliary governed by a student Board of Directors elected each year by the student body of CSUSM.
- San Marcos University Corporation
Oversees campus housing, the M. Gordon Clarke Field House and the upcoming University Student Union.