The governing board of JUPEB is chaired by the Vice-Chancellor, University of Lagos, Professor Oluwatoyin Temitayo Ogundipe (Ph.D, MBA, FLS, FRSB, FAS). Other members are:

• Vice-Chancellor of all partner universities.
• Two Vice-Chancellors of Affiliate universities (on rotation)
• Representatives of
  • The Honourable Minister of Education
  • Joint Admissions and Matriculations Board (JAMB)
  • National Universities Commission
  • The West African Examinations Council (WAEC) or National Examinations Council (NECO)
• Registrar/Chief Executive, JUPEB