Clowney, the first-overall pick in this year's NFL draft, had been dealing with a groin injury and after an evaluation, it was determined that surgery was the best option.
"We sent him to Philadelphia to have it checked out by specialists there," O'Brien said. "We decided the best thing for J.D. and the best thing for our team, and the best thing for our organization was to have sports hernia surgery. So he had that yesterday, he'll be back this afternoon."
He will miss next week's mandatory minicamp to continue rehab and anticipates a return for training camp at the end of July.
The 21-year-old former first-team All-American and SEC Defensive Player of the Year at South Carolina, Clowney was expected to return to Houston on Friday afternoon.