As a university of the California State University System, San Jose State falls under the jurisdiction of the California State University Board of Trustees and the Chancellor of the California State University. The current Chancellor is Charles B. Reed.

The chief executive of San Jose State is the President of San Jose State University. The office is currently vacant. The former President was Paul Yu, who assumed the presidency on July 15, 2004, and resigned a little over two weeks later on August 2, 2004. Officially, Yu resigned due to health reasons, but most observers believe that he resigned for other reasons. Vice President for Administration and Finance Don Kassing has been named acting president with a two-year term. The University Provost is the head of the academic affairs department of the university. Marshall Goodman "resigned" from this position in Fall 2004. Carmen Sigler took over as interim provost.

San Jose State offers 69 bachelors degrees with 81 concentrations, and 65 masters degrees with 29 concentrations.

The university has eight colleges:

• Applied Sciences & Arts [1] 
• Business [2] 
• Education [3] 
• Engineering [4] 
• Humanities & the Arts [5] 
• Science [6] 
• Social Sciences [7] 
• Social Work [8] 

as well as schools of Journalism, Library & Information Science [9] , Music & Dance, and the Office of International and Extended Services [10] , which coordinates continuing education and professional development programs.