On April 1, 2016, Stanton was featured with Ed O'Neill as part of an April Fool's joke. The joke involved deceiving viewers into believing that Ed O'Neill's character Hank from Finding Dory was the oldest and most coveted Pixar Easter egg in history.
Stanton also has a brother named Nate Stanton who is a storyboard artist at Pixar.
Stanton was born and raised in Rockport, Massachusetts. He studied character animation at The California Institute of the Arts and graduated from the school in 1983. His earliest known venture into professional animation was at Ralph Bakshi Productions, where he worked on Mighty Mouse: The New Adventures along with other young animators, such as Jeff Pidgeon, Eddie Fitzgerald, Tom Minton, John Kricfalusi, and Jim Reardon; all of them have done worthwhile things, even Pidgeon who joined him at Pixar. Stanton joined Pixar in January 1990 and was the second animator (John Lasseter being the first) and ninth overall employee hired at the studio. He now lives in Mill Valley, California and is married to Julie Stanton. He has a daughter named Audrey and a son named Ben. In addition to his direction and writing work for Pixar, he voiced Crush, the laidback turtle in Finding Nemo. According to page 17 of the book entitled Outlaw Animation: Cutting-Edge Cartoons from the Spike and Mike Festivals by Jerry Beck, Stanton was also friends with famed animation promoters "Spike and Mike". In one particular instance, Spike visited Stanton's home in a superhero costume, calling himself "the Centaur". After frightening the neighborhood parents and captivating the imaginations of the children near an ice cream truck Stanton had to get Spike back inside before anyone alerted the authorities. In an interview with World Magazine's Megan Basham, Stanton explained his singular vision for WALL-E: "What really interested me was the idea of the most human thing in the universe being a machine because it has more interest in finding out what the point of living is than actual people. The greatest commandment Christ gives us is to love, but that's not always our priority. So I came up with this premise that could demonstrate what I was trying to say—that irrational love defeats the world's programming. You've got these two robots that are trying to go above their basest directives, literally their programming, to experience love." Stanton later worked on his first live-action film called John Carter, which was released in 2012 by Walt Disney Pictures, albeit to mixed reception. He also directed the long-anticipated Finding Nemo sequel Finding Dory.