"Just like at home, honey," Stiller said to his wife, actress Christine Taylor, on Friday as he put on the female attire.
The event was organized by the Hasty Pudding Theatricals, the nation's oldest undergraduate drama troupe.
Stiller, 41, played along with the good-natured traditional Hasty Pudding roast, which lampooned his career. He won the award decades after dropping out of film school at the University of California, Los Angeles.
"For somebody who never could have ever got close to getting into Harvard, I think that this was even better — so I thank you very much," Stiller said.
The awards are given to performers who have made a "lasting and impressive contribution to the world of entertainment," according to the drama troupe.
"Ben Stiller has really pioneered in many ways, news forms of comedy," Joshua Lachter, the press and publicity manager for the Hasty Pudding Theatricals, said in a telephone interview with The Associated Press.
Scarlett Johansson received the Hasty Pudding Woman of the Year award last week. Last year's honorees were Halle Berry and Richard Gere.