Johnson was born in Elizabeth, New Jersey on August 24, 1945. She was one of seven children. Her father, Malcolm Michaels Sr, worked for General Motors. Her mother, mother, Alberta Claiborne, was a housekeeper. Johnson attended an African Methodist Episcopal Church as a child. Johnson was very religious. She was very interested in Catholicism, and kept a private altar at home. Johnson began wearing dresses at the age of five but stopped due to bullying from boys in her neighborhood. Johnson did not come to terms with being gay until the age of 17. Her mother was reportedly very homophobic, but Johnson has said that her mother was unaware of the LGBT community. After graduating from high school, Johnson moved to Greenwich Village, New York on her own. She supported herself by waiting tables. After meeting other gay people in the city, Johnson gained the confidence to come out herself.