The How I Met Your Mother star will be at the helm of the prestigious event for the third time.
The show honours the best of Broadway and theatre which will give Neil an opportunity to show off his singing and dancing skills.
"I'm thrilled to be a part of this year's Tony Awards," the Doogie Howser, M.D. star said 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 five!"
Neil's hosting duties in 2009 led to him winning an Emmy Award for the successful telecast.
The 38-year-old has also appeared in Broadway shows Proof and musicals Cabaret and Assassins.
CBS Entertainment's Jack Sussman called Neil "the ultimate showman."
"He brings great talent, energy and creativity to the Tony stage and usually a surprise or two. I can't wait to see what he has in store this year."
The 2012 Tony Awards will broadcast live on June 10 from New York's Beacon Theater.