The system, headquartered in Tallahassee,[2] is overseen by a chancellor and governed by the Florida Board of Governors.

Prior to 1905, Florida's state institutions were governed by a Board of Education and even earlier variations thereof, reaching back to the Florida Constitution of 1838 wherein higher education and normal education was established, based on grants of land from the U.S. Congress.

From 1905 to 1965, the few universities in the system were governed by the Florida Board of Control.

The Board of Regents governed until it was disbanded by the Florida Legislature in 2001, and its authority was divided between the Florida Board of Education (which was given some authority over all levels of public education in the state), and appointed university boards of trustees, which operated independently for each separate institution.

In 2002, Floridians led by U.S. senator Bob Graham passed an amendment to the Florida Constitution establishing a new statewide governing body, the Florida Board of Governors.