Born in Chicago, Illinois, John Musker became fascinated with comics and cartoons, especially Disney classics such as Sleeping Beauty and Pinocchio, at an early age. By the time he was eight, he knew he wanted to become an animator. In high school, Musker was a cartoonist for the school paper, and at Northwestern University, where he majored in English, he drew cartoons for the Daily Northwestern. After graduating in 1974, he headed to California to pursue his dream of working for the Disney studios. His initial interview with Disney was met with rejection, so he enrolled with a partial scholarship to the California Institute of the Arts to perfect his craft. Completion of his first year of study at CalArts included a summer internship at Disney, and they were so impressed with his work for them that they offered him a full time job as an animator. Musker turned it down, opting instead to return for his second year of training.

He finally began his career at Disney in 1977. His first assignment was as an assistant animator on a short called The Small One. His feature film debut came when he worked as an animator on Pete's Dragon (1977). He was promoted to supervising animator by 1981, when he worked on The Fox and the Hound(1981).

Soon after, he began collaborating with Ron Clements, another Disney animator, and the two provided additional story material for The Black Cauldron (1985). In 1986, along with other collaborators, they wrote and directed The Great Mouse Detective, based on a short Clements had made earlier.

Clements and Musker next co-directed The Little Mermaid (1989), based on the fairy tale by Hans Christian Anderson. The award-winning movie was a huge hit for Disney, and the team next wrote, directed and produced Aladdin (1992), another enormous success for the studio that went on to become one of the most popular animated films of all time. It was nominated for many awards, including several Oscars® and even won a couple, for Best Music and Best Song.

Their next project was Hercules (1997), which they directed, wrote and produced, and although it wasn't as big a hit as their previous films, they won an Annie award together for "Best Individual Achievement: Directing in a Feature Production."

Musker and Clements shared another Annie nomination for "Outstanding Directing in an Animated Feature Production" for 2002's Treasure Planet, but it was in 2010 that they were nominated for the biggest prize of all, an Academy Award for their work on The Princess and the Frog. Though the film didn't win in any of the three categories it was nominated for, it picked up several Annies and was a box office success.

Musker and his wife Gale, whom he met at Disney, have three children.