Under the Office of the President, the administration of CSU San Marcos is comprised of four divisions:

In addition, the University has a long-standing cooperative relationship with the University Auxiliary and Research Services Corporation (UARSC), a non-profit auxiliary that oversees campus amenities such as food service and bookstores.

Another important affiliate to the university is Associated Students, Inc. ASI is a non-profit, student-run auxiliary governed by a student Board of Directors elected each year by the student body of CSU San Marcos.