The history of the college can be traced back to March 1987, when the foundation Vice Chancellor of Lagos State University, Prof. Afolabi Olumide, set up an advisory board in an attempt to establish the Lagos State University College of Medicine, based on the recommendation of the Tertiary Education Review Committee.

Although the advisory board submitted its report in 1987, the problems faced by the University at the time delayed the establishment of the College of Medicine.

The University went through hard periods during the successive administrations headed at different times by Prof. Jadesola Akande and Prof, Enitan Bababunmi as Vice-Chancellors.

The advisory committee submitted its report to the military administrator, Col. Muhammed Buba Marwa, in August 1997.

In two decades, the college has witnessed rapid administrative and infrastructural transformation in terms of building structures, equipment, facilities as well as significant increase in personnel.