Born in Marshall, Texas, Farmer was an excellent student who skipped several grades in elementary school. At fourteen he attended Wiley College where his father taught. Farmer graduated in 1938, and then attended to Howard University's School of Religion. He graduated from Howard in 1941. When World War II began the pacifist Farmer refused to serve, especially in a segregated army. He opposed war in general, and more specifically objected to serving in the segregated armed forces. Farmer was deferred from the draft because he held a divinity degree. Farmer decided to fight the Methodist Church's policy of segregation rather than become an ordained minister.
In 1942 Farmer founded the Congress of Racial Equality or CORE, a pacifist organization dedicated to achieving racial harmony and equality through non-violence. In 1961 Farmer became the first national director of CORE. Though by the mid 1960's Farmer was growing disenfranchised with emerging militancy and black nationalist sentiments in CORE and in 1966 resigned.
He took a teaching position at Lincoln University and continued to lecture. In 1968 Farmer ran for U.S. Congress as a Republican, but lost to Shirley Chisholm. However his defeat was not total, the recently elected President, Richard Nixon, offered him the position of Assistant Secretary of Health, Education, and Welfare.
Farmer retired from politics in 1971, but remained active lecturing and serving on various boards and committees. He published his autobiography, Lay Bare the Heart, in 1985. Farmer live to see CORE move closer to its centrist roots the 1980s and 1990s. President Bill Clinton awarded him the Congressional Medal of Freedom in 1998.