In 1935, he got a job as a background and layout artist at Disney, where he worked on such classic films as Snow White and the Seven Dwarfs, Pinocchio, Dumbo, and Bambi, as well as "The Rite of Spring" segment from Fantasia. He left the company during the 1941 animator's strike, and found work directing films for Screen Gems and the Army's First Motion Picture Unit until he founded United Productions of America. UPA soon became famous for their highly stylized designs and limited animation.
He was forced to leave UPA in 1952 when he refused to name names before the House Committee on Un-American Activities. He founded Storyboard Studios the next year and worked on commercials (where he would not be credited), but was forced to turn down more exciting projects (such as an adaptation of Finian's Rainbow) because his name was still blacklisted. He moved his studio to New York in 1955, where he switched production over to independent short films.
He married Faith Elliott (September 16, 1924 – December 7, 2001) the same year, and they collaborated on nearly every film he made until his death in 1977 at age 62 during heart surgery; their final production was A Doonesbury Special (with creator Gary Trudeau), which aired on NBC in November of that year. Faith and their four children carried on his legacy in the renamed Hubley Studios. John is survived by his daughters Georgia Hubley, who plays drums and sings for the critically acclaimed rock band, Yo La Tengo as well as Emily Hubley, a filmmaker and animator, who has made numerous short films, including animated inserts and segments for documentaries such as Blue Vinyl, and the film version of Hedwig and the Angry Inch.