The prize presentation is scheduled to take place May 31 at the Gibson Amphitheatre with comedian Andy Samberg as host.
Stiller's film credits include "Reality Bites," "There's Something About Mary," "Meet the Parents, "Dodgeball: A True Underdog Story," "Tropic Thunder" and "Night at the Museum: Battle of the Smithsonian."
Past recipients of the Generation Award include Adam Sandler, Mike Myers, Tom Cruise and Jim Carrey.
"From 'The Royal Tenenbaums' to 'Zoolander,' Ben is a comedic chameleon, able to make the leap between drama and full-out comedy while maintaining his own unique brand of subversive humor," Van Toffler, president of MTV Networks Music/Logo/Film Group, said in a statement. "That versatility and talent has earned him legions of devoted fans over the years which makes him a perfect recipient for the MTV Generation Award. Whether it's fighting a monkey in a museum or licking a decapitated head, nothing is ever off-limits for him and that's the type of warped creative vision and commitment MTV loves to reward."
"I am honored to be getting the Generation Award," added Stiller. "I was given my first show at MTV, and also canceled for the first time. I also was secretly having an affair with J.J. Jackson, so it brings back pleasant memories."