A national consultation, convened by the Union Ministry of Health and Family Welfare in September 2004, recommended a foundation which could rapidly advance public health education, training, research and advocacy.

The Government of India enabled the setting up of PHFI in 2006 in response to the limited public health institutional capacity and the foundation was established to strengthen training, research and policy through interdisciplinary and health system connected education and, policy programme relevant research, evidence based & equity promoting policy development, affordable health technologies, people empowering health promotion & advocacy for prioritised health causes in the area of Public Health.

[citation needed] PHFI lost FCRA status in 2017 for lobbying against tobacco activities and was banned from receiving foreign funds.

[2] [3] PHFI has established five Indian Institutes of Public Health (IIPHs) in Bhubaneswar, Delhi, Gandhinagar, Hyderabad and Shillong.

In 2015 Indian Institute of Public Health, Gandhinagar was the first IIPH to be granted autonomous university status through The Indian Institute of Public Health Gandhinagar Act, 2015 laid out by the State Government of Gujarat.