East African countries have a long history of cooperation in cultural and socioeconomic areas. Between 1947 and 1967 the cooperation was facilitated by East Africa (High Commission) Orders in Council. The establishment of the East African Common Services in 1961, resulted in an important milestone for cooperation in health; the establishment of the East African Medical Research Council (EAMRC) in 1962. The EAMRC was established through the enactment of Act No 14 of 1962, which was signed on behalf of the East African Common Services, with the advice and consent of the East African Central Legislative Assembly, by H.E. Julius Nyerere, the President of Tanganyika; Hon. W.F. Coutts, the Governor-General of Uganda; and Hon. Malcolm MacDonald, the Governor of Kenya. The Council, with its headquarters in Arusha, Tanzania was established to be responsible for the coordination of medical research and related subjects in East Africa; and in particular to be responsible for determination of the desirable priorities to be applied to the activities of the East African Common Services, and towards avoidance of duplication of efforts. Under the EAMRC, five specialised research institutions were established, namely: the East African Institute for Medical Research; the East African Institute of Malaria and Vector-borne Diseases; the East African Virus Research Institute; the East African Trypanosomiasis Research Organisation; and the East African Leprosy Research Centre. The institutions operated across the entire East African region and were hosted by each of the three member states.

The Treaty for the establishment of the East African Cooperation (EAC) in 1967 strengthened further the cooperation of the member states and incorporated the EAMRC and its institutions. Subsequent to the collapse of the EAC in 1977, the functions of the EAMRC and its institutions were relinquished to the member states. This resulted in the formation of the national research institutions, namely; National Institute for Medical Research (NIMR), Tanzania; Kenya Medical Research Institute (KEMRI), Kenya; and Uganda Virus Research Institute (UVRI), Uganda. Formation of the national institutions is a success story, to-date they have grown into well-coordinated networks of national research centers in their respective countries. They have broadened their mandate to include conduct and coordination of medical research, capacity development, and guiding national health policies and practices. They contribute to resource mobilisation and have established international links and collaborations.

The re-establishment of the EAC in 1999, as part of the Treaty, revived the regional coordination of medical research by establishing the East African Health Research Commission (EAHRC) in 2008. The EAC broadened the EAHRC mandate from the defunct EAMRC. The EAHRC became the mechanism for making available to the EAC, advice upon all matters of health and health-related research that are necessary for; knowledge generation, technological development, policy formulation, and practice.
The National Research Institutions became the national focal points for coordination of the EAHRC activities and link with stakeholders at the national level. When the Republics of Burundi and Rwanda joined the EAC in 2007, naturally their national research institutions; Institut National de Sante Publique, and Rwanda Biomedical Centre became the EAHRC national focal points, respectively.

The EAHRC was officially operationalised in July 2015, when the first three staff were appointed. This is the general overview of the EAHRC and some of its regional strategic programmes since 2015.