Farmer was educated at Wiley College in Marshall, Texas (1938), and at Howard University in Washington, D.C. (1941), where his father taught divinity. A conscientious objector on religious grounds, he received a military deferral in World War II, and he joined the pacifist Fellowship of Reconciliation (FOR). In 1942 he cofounded CORE, which originated integrated bus trips through the South, called Freedom Rides, to challenge local efforts to block the desegregation of interstate busing. Farmer, who sought racial justice by means of nonviolence, was often a target of racial violence himself.

He resigned from the leadership of CORE in 1965, and in 1968 he lost a run for a seat in the U.S. House of Representatives to Shirley Chisholm (Chisholm, Shirley). In 1969–70 he served as assistant secretary of health, education and welfare under President Richard M. Nixon. In 1985 Farmer published his autobiography, Lay Bare the Heart, and in 1998 he was awarded the Presidential Medal of Freedom.