The College was formally established by the University of Maiduguri act 83 of 1979 comprising four faculties, namely; Basic Medical Sciences, Allied Health Sciences, Clinical Sciences and Dentistry with Late Professor George Miller Edington as its founding Provost. Among the pioneer members of its academic staff were Professor D. B. Grillo (Department of Anatomy), Professor J. K. Segupta (Department of Physiology), Dr. P. K. Joseph (Department of Biochemistry) and Professor Harold Scarborough (Department of Medicine). On the sad demise of Professor G. M. Edington in January 1981, Professor H. Scarborough succeeded him as the second Provost of the College. The former was credited for the sound planning and developing the Pre-clinical Departments of Anatomy, Physiology and Biochemistry. After his death, the task fell on Professor Scarborough to start the Clinical Department, initially using the General Hospital, Maiduguri and later moved into the new Teaching Hospital at the beginning of 1982. The mature academic leadership of Professor Scarborough put the College on a sound footing and the first set of 21 Doctors - maiden products of the College graduated in June 1983.
Professor Scarborough retired from the services of the University in 1984 and was succeeded by Professor S. B. Lagundoye, Professor of Radiology, University of Ibadan on secondment as the third substantive Provost of the College. He remained at the helm of affairs until October 1987 before going back to the University of Ibadan. He was succeeded by numerous acting Provosts at different times namely: Professor K. Ahmad, Head, Department of Pharmacology for about six months (1987-1988), Professor H.C. Varma, Head, Department of Human Anatomy (1988-1989), Professor A. N. Sawhney, Head, Department of Microbiology (1989-1991; 1994-1995). The situation stabilized with the assumption of office of the following Provosts:
Professor Umaru Shehu, 1992-1993. (Acting)
Professor I.I. Onyewotu, 1993-1994.
Professor I. Mohammed, 1995-2000.
Professor M.I.A. Khalil, 2000-2004.
Professor. Wazirin Abba Hassan, 2004-2008.
Professor A. Tahir, 2008-2010.
Professor U.H Pindiga, 2010-2011.
Professor Dilli Dogo, 2011 to 2015. (Acting)
Professor Ahmed Ahidjo 2015 to 2018.
Professor Mohammed Bukar 2018 till date.
The main functions of the College include teaching, research and community service. Teaching and training of Medical Doctors and allied health workers to meet high international standards is one of the most important objectives of the College. A Medical Doctor trained in this institution is expected to be well versed in Medical and Health problems of Africa in general and Nigeria in particular. Their training includes preventive medicine and community based - Primary Health care.
The College has continued to grow since inception. It witnessed the introduction of programmes including Degrees in Human Anatomy, Dentistry, Medical Laboratory Science, Medical Rehabilitation and Nursing Science. All these departments are accredited by the national universities commission (NUC) and their professional bodies. The College in 2018 began to operate the full collegiate system with five faculties, namely; Allied Health Sciences, Basic Medical Sciences, Basic Clinical Sciences, Clinical Sciences and Dentistry.