By the 1900s, First Nations and Inuit communities were decimated by smallpox, tuberculosis, and other communicable diseases, but little coordinated effort existed on a national level to address the health crisis. In 1904, the Department of Indian Affairs appointed a general medical superintendent to start medical programs and develop health facilities.
In 1945, the Department of National Health and Welfare was created. Medical Services Branch was formed in 1962 by merging Indian Health and Northern Health Services with other independent federal field services.
In 1974, the Minister of National Health and Welfare tabled the Policy of the Federal Government concerning Indian Health Services. The policy reiterated that no statutory or treaty obligations exist to provide health services to Indians. However, the federal government wanted to ensure "the availability of services by providing it directly where normal provincial services (were) not available, and giving financial assistance to indigent Indians to pay for necessary services when the assistance (was) not otherwise provided".
In 1979, a new Indian Health Policy was announced. It stated that uninsured benefits would rely upon "professional medical and dental judgment." The policy also recognized the need for community development, a strong relationship between Indian people, the federal government, and the Canadian health system.
Medical Services Branch started to work towards transferring control of health services to First Nations and Inuit communities and organizations in the mid-1980's through the Strategic Policy, Planning and Analysis Directorate.
After the Royal Commission on Aboriginal Peoples was released, the federal government announced Gathering Strength - Canada's Aboriginal Action Plan. In the action plan, Health Canada is committed to diabetes and tuberculosis initiatives, developing the Aboriginal Healing Foundation and a healing strategy addressing the legacy of Indian residential schools, in partnership with the Department of Indian Affairs.
In 2000, the Medical Services Branch was renamed the First Nations and Inuit Health Branch.