This will be the third time that Harris has hosted the telecast, following his work on both the 63rd Annual Tony Awards in 2009, and the 65th Annual Tony Awards in 2011.
As he did in 2011, Harris will also act as a producer, along with executive producers Ricky Kirshner and Glenn Weiss of White Cherry Entertainment.
The Tony Awards will air live on CBS from 8 PM-11 PM ET. The American Theatre Wing's Tony Awards are presented by The Broadway League and the American Theatre Wing.
"I'm thrilled to be a part of this year's Tony Awards,” said Harris in a statement. “Not only will I be shining a spotlight on the best that Broadway has to offer, but hopefully I'll score some free house seats to a show or 5."
"We're excited to be working once again with the extremely talented Neil Patrick Harris,” said Kirshner and Weiss. “Last year's show was such a success and we can't wait to bring it to new heights this year!"
Harris has been seen on Broadway in Assassins, Proof and Cabaret. He also starred in the New York Philharmonic production of Company. The performer is the winner of two 2010 Emmy Awards and was nominated for his work on the CBS series "How I Met Your Mother."