AFMC when conceived began as postgraduate training and research center. The first commandant of the institution was Col PP Chowdry. The foundation stone of the main building was laid on 3 April 1953 (erstwhile AMC anniversary day) by Lt Gen DR Thapar, the then Director General, Armed Forces Medical Services, and was completed in August 1956. The role of the college was enlarged when the department of Dental Surgery was added in May 1955.

The graduate wing was started on 04 Aug 1962, Mr VK Krishna Menon inaugurated the undergraduate wing. The College of Nursing was added in 1964.

The college celebrated its golden jubilee in 1998 with pride. The Golden Jubilee block housing eighteen departments was inaugurated by Shri George Fernandes, defense minister in 1998. AFMC has found a place amongst the best medical colleges in the country and is widely acknowledged to be a premier national institute.