Haynes was born January 2, 1961, in Los Angeles, and grew up in the city's Encino neighborhood. His father, Allen E. Haynes, was a cosmetics importer, and his mother, Sherry Lynne (née Semler), studied acting. Haynes is Jewish on his mother's side. His younger sister is Gwynneth Haynes of the band Sophe Lux.
Haynes developed an interest in film at an early age, and produced a short film, The Suicide (1978), while still in high school. He studied art and semiotics at Brown University, where he directed his first short film Assassins: A Film Concerning Rimbaud (1985), inspired by the French poet Arthur Rimbaud (a personality Haynes would later reference in his film I'm Not There). At Brown, he met Christine Vachon, who would go on to produce all of his feature films. After graduating from Brown, Haynes moved to New York City and became involved in the independent film scene, launching Apparatus Productions, a non-profit organization for the support of independent film.
According to Cinematic/Sexual: An Interview with Todd Haynes, in response to whether his academic background affected his film-making practice, Haynes stated that his high school teacher taught him a valuable lesson: "Reality can't be a criterion for judging the success or failure of a film, or its effect on you. It was a simple, but eye-opening, way of approaching film."