The Texans selected Clowney with the No. 1 overall pick in this year's draft. The 6-foot-5, 266-pound outside linebacker has played in only four games this season, recording seven total tackles and zero sacks.
O'Brien commented on the news: "I think highly of all these players here... As it relates to JD, this guy's been injured and it's time to clean it up," he said.
The announcement comes after Clowney met with Dr. James Andrews about the knee.
He missed six games after undergoing surgery to repair a torn meniscus in Houston's season-opening victory over the Washington Redskins and returned for the team's Oct. 26 victory over the Tennessee Titans.
Houston is 6-6 and in second place in the AFC South.
- Chris Johnson