The actor's involvement in the latest instalment of the animated franchise was announced at Disney's Comic-Con panel.
Toy Story 3 is scheduled for release in summer 2010.
"Barbie is back, and this time she plays a bigger role. So naturally we had to bring in her companion Ken this time," said director Lee Unkrich.
"And we can announce today that he's voiced by Michael Keaton. He worked with us on Cars, where he voiced the bad guy, and he was a blast to work with so we invited him back as Ken."
Keaton will also apparently conduct a faux-interview with Ken, where his character gets upset at accusations that his girlfriend Barbie is the bigger star. The interview is expected to appear as a DVD extra.