Johnston got his start in 1977, as a concept artist and effects technician for George Lucas' first Star Wars movie. He continued working with Lucasfilm on the next two Star Wars movies, along with the first two Indiana Jones movies (earning an Academy Award for Best Visual Effects for his work on Raiders of the Lost Ark).
In 1989, Johnston made the leap to director with the Disney film, Honey, I Shrunk the Kids. He also directed The Rocketeer and the Touchstone Pictures film, Hidalgo. Additionally, he directed additional scenes for The Nutcracker and the Four Realms, as Lasse Hallström was unavailable to do the reshoots.