The Board of Trustees is the constitutional governing body of the State Institutions of Higher Learning. Because of changes to the legislation regarding the appointment of Board members, "after January 1, 2004, as vacancies occur, the twelve-member Board shall be appointed from each of the three Mississippi Supreme Court districts until there are four members from each Supreme Court district. The terms of office are reduced from twelve years to nine years. The terms are staggered so that all members appointed after 2012 will have a term of nine years."

The Board Office, located in the Education and Research Center of Mississippi, is responsible for policy and financial oversight of the eight public institutions of higher learning.

The Commissioner of Higher Education is responsible for assisting the Board in the administration of the Board's policies and bylaws. Divisions of the Commissioner's Office include academic and student affairs, construction and physical affairs, finance and administration, and research and planning. The Board oversees degree-credit courses, research and public service activities and programs at the eight public universities, including The University of Mississippi Medical Center, The Mississippi State University Division of Agriculture, Forestry and Veterinary Medicine, ten off-campus centers, and various other locations throughout the state. Available programs range from a variety of undergraduate disciplines to most professional fields. All eight universities offer master's level programs, six have programs at the education specialist level and five offer doctoral-level programs.