The Pixar movie uses five characters to personify the emotions of a girl named Riley as her parents move from the Midwestern state of Minnesota to California.
"When I was in junior high, literally my goal was to make it through the day with no one noticing me," said Docter, himself a Minnesota native.
"Obviously, something went horribly wrong tonight," he told the star-studded Hollywood crowd.
"But the point is - we felt like growing up was really hard, and that's a worthy subject to make a movie about," he said.
"Inside Out" beat out a field that included "Anomalisa," director Charlie Kaufman's critically acclaimed puppet noir story of a miserable business traveler, and "Shaun the Sheep Movie," the latest in British animator Nick Park's "Wallace and Gromit" offbeat comedy series.
Docter, whose films are released by Disney, was also the creator of the popular animated flicks "Monsters, Inc." and "Up." "Up," the 2009 story of a retiree's adventures with a boy, was the second animated film to be nominated for the best picture Oscar, the film industry's most prestigious prize.
Both "Up" and "Inside Out" were produced by Jonas Rivera.