The team used the non-exclusive franchise designation, meaning a team can sign Clowney to an offer sheet once free agency begins next week but would have to surrender two first-round draft picks if the Texans choose not to match it.
"Today, we have placed the franchise tag on Jadeveon Clowney, but our goal is to continue to work with his representation on a long-term contract," Texans general manager Brian Gaine said in a statement. "This gives us both an opportunity to continue to do so."
Teams have until July 15 to reach a long-term contract with a tagged player. If not, an extension would have to wait until after the regular season.
The Texans opted to let the first overall pick of the 2014 draft play on his fifth-year option in 2018 -- at a base salary of $12.306 million -- rather than sign him to a long-term deal, although Gaine said at the time there were discussions about an extension before the season.
The Texans did not specify a position for Clowney when announcing the move. The one-year franchise tag is projected to be worth $17.128 million for defensive ends. The tag for linebackers is expected to be $15.443 million.
According to ESPN Stats & Information, Clowney played most of his snaps at defensive end in 2018. He logged 729 at defensive end, 101 at defensive tackle and 33 at linebacker last season.
Clowney, who was named to his third consecutive Pro Bowl last season, finished the 2018 season with 47 tackles, nine sacks, a forced fumble and a fumble recovery. He also had 16 tackles for loss, which tied for ninth in the NFL last season, and he now has 53 tackles for loss over the past three seasons, which ranks third in the league.
The 26-year-old Clowney struggled with knee injuries early in his career, missing 15 games in his first two seasons. In 2016, he played through wrist and elbow injuries, appearing in 14 games and making the Pro Bowl for the first time. Since then, he has missed just one game over two seasons.
Texans coach Bill O'Brien praised Clowney in his end-of-season news conference, saying he understands the NFL is a business, but that he thinks "very highly" of Clowney.
"I think he's a disruptive player," O'Brien said. "Jadeveon is a big part of what we've done here. Like I always say, when he feels good, health-wise, and he's ready to rock and roll, he's hard to handle."