Phelps, whose 14 Olympic gold medals include his unprecedented eight from the 2008 Beijing Games, raced for the first time since August last month in another event on the US tour in Austin, Texas.
Other US Olympic champions at the Indianapolis meet will include Ryan Lochte and Jason Lezak.
A strong field of international swimmers will also compete, including Japanese Olympic gold medallist Kosuke Kitajima, Austrian Olympic runner-up Markus Rogan, South African Olympian Darian Townsend and Swiss Olympian Dominick Meichtry.
The meet serves as part of a tune-up series ahead of the World Championships in Shanghai in July.