Johnson studied at Northwestern University where he earned a BA in English Literature. He also produced two animated films; both of which earned Richard Grant Organization Awards.
Upon graduating, he worked for two years as a freelance animator and director. His introduction to computer animation came in 1985 while he worked on the staff at Post Effects in Chicago. He later joined Pacific Data Images (PDI) in 1988 and two years later co-founded the studio's Character Animation Group. He also directed the first CG Pillsbury Doughboy commercial.
Johnson won two Annie awards on Antz and Over the Hedge, an Audience Award on Over the Hedge, and a Grand Prize for The Simpsons' "Treehouse of Horror VI".
He served as executive producer for How to Train Your Dragon in 3D.
He has most recently served as the director of the Kung Fu Panda Holiday Special, and is set to direct for DreamWorks Animation a 2014 animated feature film adaptation of The True Meaning of Smekday, titled Happy Smekday!.