Coach Bill O'Brien disclosed the procedure Friday and said Clowney had been struggling with a groin issue. O'Brien said the standout from South Carolina was sent to a specialist in Philadelphia.
''We decided the best thing for (Clowney) and for the best team for our team and the best thing for the organization was to have sports hernia surgery,'' O'Brien said.
The surgery was performed Thursday. O'Brien expects Clowney to be ready for training camp, which begins in late July.
O'Brien wasn't sure exactly how long he's been dealing with this issue.
''I don't think it was too long,'' O'Brien said. ''I think it wasn't too long, but again you know, we looked at it as let's take care of it now and he will be ready to go for training camp.''
Clowney signed a four-year contract with the Texans a week ago. Houston has an option for a fifth year, as in all NFL contracts with first-round picks under the current collective bargaining agreement.
The defensive end will play outside linebacker in Houston's 3-4 scheme. The 6-foot-5, 266-pound Clowney is expected to pair with 2012 Defensive Player of the Year J.J. Watt to boost Houston's already solid pass rush. Clowney had 47 tackles for losses and 24 sacks in a three-year career at South Carolina. He has said he doesn't think the transition to linebacker in Houston will be that difficult.
Clowney is the third top overall pick in team history. Houston selected quarterback David Carr in 2002 and defensive end Mario Williams in 2006.
The Texans have their mandatory mini-camp next week and all eyes are on star receiver Andre Johnson and if he'll actually skip the practices after saying he would last month. He hasn't attended any of Houston's voluntary workouts this offseason after saying: ''I just kind of wonder sometimes: 'Is this still the place for me?'''
O'Brien was asked if he expects the 11-year veteran and longest tenured Texan to attend mini-camp.
''I don't know,'' O'Brien said. ''I don't know.''