The Institue was initially known as National Institute for Medical Research. It was formally established by the Federal Military Government through the Research Institute (Establishment) order of 1977, pursuant to the National Science and Technology Development Agency Decree (No 5) of 1977.
Its immediate predecessor was the Medical Research Council of Nigeria (A name by which many still erroneously refer to the Institute) which was created by Decree No. 1 of 1972. Prior to this, Medical Research had been carried out in the Insitutet since 1920 with the arrival of the colonial medical research team named "the Rockefeller Foundation, Yellow Fever Commission to the West Coast of Africa".
The West African Yellow Fever Commission arrived in 1925 and built a Research Unit in Yaba. Subsequent to these, the West African Council for Medical Research was established in 1954. Although NIMR inherited the assets of the Medical Research Council of Nigeria, its powers and functions were more restricted in line with creation then of the National Science and Technology Development Agency, which was transformed into the Ministry of Science, and Technology in 1979.
NIMR remained the only Institute concerned with research into human Medicine until the establishment of the National Institute for Pharmaceutical Research and Development in Abuja.
Currently, NIMR is a goverment parastatal under Ministry of Health. It has five research divisions, three non research divisions, several support units and research laboratories.
