Miyazaki, the second of four brothers, was born in the town of Akebono-cho, part of Tokyo's Bunkyō-ku. During World War II, Miyazaki's father Katsuji was director of Miyazaki Airplane, owned by his brother (Hayao Miyazaki's uncle), which made rudders for A6M Zero fighter planes. During this time, Miyazaki drew airplanes and developed a lifelong fascination with aviation, a penchant that later manifested as a recurring theme in his films.

Miyazaki's mother was a voracious reader who often questioned socially accepted norms. Miyazaki later said that he inherited his questioning and skeptical mind from her. His mother underwent treatment for spinal tuberculosis from 1947 until 1955, and so the family moved frequently. Miyazaki's film My Neighbor Totoro is set in that time period and features a family whose mother is similarly afflicted.

Miyazaki attended Toyotama High School. In his third year there, he saw the film Hakujaden, which has been described as "the first-ever Japanese feature length color anime." His interest in animation began in this period; however, in order to become an animator, he had to learn to draw the human figure, since his prior work had been limited to airplanes and battleships.

After high school, Miyazaki attended Gakushuin University, from which he would graduate in 1963 with degrees in political science and economics. He was a member of the "Children's Literature research club," the "closest thing to a comics club in those days."

In April 1963, Miyazaki got a job at Toei Animation, working as an in-between artist on the anime Watchdog Bow Wow (Wanwan Chushingura). He was a leader in a labor dispute soon after his arrival, becoming chief secretary of Toei's labor union in 1964.

In October 1965, he married fellow animator Akemi Ota, who later left work to raise their two sons, Gorō and Keisuke. Gorō is now an animator and filmmaker, and has directed Tales from Earthsea at Studio Ghibli. Keisuke is a wood artist who has created pieces for the Ghibli Museum and who made the wood engraving shown in the Studio Ghibli film Whisper of the Heart.

Hayao Miyazaki's dedication to his work has often been reported to have impacted negatively his relationship with his son Gorō. He has expressed that he doesn't wish to create a dynasty of animators and that his son has to create a name for himself.