The Faculty was upgraded to the current designation from the original status of School of Clinical Sciences by the approval of the Governing Council of the University of Lagos at its meeting held on the 25th of November 2009, in line with the collegiate system recommended by the National Universities Commission. The conversion occurred during the tenure of a former Vice Chancellor of the University ,Prof. Tolu Odugbemi, PNMC, OON, NNOM, FAS and the past Provost of CMUL, Prof. ‘Wole Atoyebi. Historically, the origins of the Faculty date back to the establishment of the Medical School which was inaugurated by the passage of the University of Lagos Act in 1962 by the Federal Parliament (redesignation of the Medical School to College of Medicine was done in March, 1967). Since its inception, the Faculty has graduated several thousands of students from its various academic programs and is a significant contributor to the healthcare industry pool of employable high-quality graduates.

The Faculty is the largest of the faculties in the College and the University and is comprised of 13 departments employing over 150 fulltime academic staff.