This will be Harris' fourth time hosting the Tony Awards. The "How I Met Your Mother" star hosted the show last year, in 2011 and 2009. He will also act as producer, alongside executive producers Ricky Kirshner and Glenn Weiss.
In a statement released on Thursday, Harris said this year's show will be "more impressive than ever."
The award show, which honors the best of Broadway, is scheduled for June 9. The show is produced jointly by the Broadway League and the American Theatre Wing.
Last year's show at the Beacon Theatre was seen by 6 million viewers. That figure is significantly down from 2011's 6.9 million. The 2011 show was also the second-lowest ratings for the Tony Awards since 1988.
Harris, 39, has starred in three Broadway productions, including "Assassins," ''Proof," opposite Anne Heche, and as the exuberant master of ceremonies in "Cabaret."
The Associated Press contributed to this report.