CBS is to broadcast the Broadway prize presentation live from Radio City Music Hall on June 7.
The Tonys are presented by The Broadway League and The American Theatre Wing.
Harris is best known for his roles in the TV shows "How I Met Your Mother" and "Doogie Howser, M.D.," as well as for his performances in the stage productions of "Assassins," "Cabaret" and "Proof."
"The discipline of live theater -- doing the same perfect thing night after night, eight times a week -- never ceases to amaze me," Harris said in a statement. "I'm truly honored to have been chosen as the Master of Ceremonies for this year's Tony Awards, and I hope to help provide a first-class evening for all."
"We are thrilled to being working with Neil on the most important theater night of the year. His love for Broadway and great knowledge of theater combined with his on-stage presence makes him the perfect person to guide us through what is sure to be a great night," added Ricky Kirshner, executive producer of the Tony Awards telecast.