Miyazaki's mother was a voracious reader and an intelligent woman, who often questioned socially accepted norms. Miyazaki later said that he inherited his questioning and skeptical mind from her.

Miyazaki moved frequently throughout his childhood, in part because his mother was undergoing treatment for spinal tuberculosis from 1947 until 1955. Miyazaki's film My Neighbor Totoro features a family whose mother is similarly afflicted.

In about 1956 - the date is apparently uncertain - Miyazaki entered Toyotama High School. In his third year there, he saw the film Hakuja Den, described as "the first-ever Japanese feature-length color anime", and began to take an interest in animation. In order to become an animator, he had to learn to draw people, because his artwork up until that point had been limited to drawing airplanes and battleships.

After high school, Miyazaki attended Gakushuin University, graduating in 1963 with degrees in political science and economics. He was a member of the "children's literature research club," said to be "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 Wanwan Chushingura (Watchdog Bow Wow). He was a leader in a labor dispute soon after his arrival, and he became 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, Goro and Keisuke. Goro is now an anime filmmaker himself, directing Tales from Earthsea at Studio Ghibli. Keisuke is a wood artist who has done work for the Ghibli Museum and who made the wood engraving shown in Ghibli's Whisper of the Heart.