On July 13, 2003, he was traded to the San Diego Padres for Matt Herges.
On April 5, 2005, he was suspended 15 games for testing positive for steroids while pitching in the minor leagues.
Later that season, he was called up from the Triple-A Portland Beavers.
He emerged as a vital figure in middle relief, not allowing a home run in 47.2 innings.

In 2006, Hensley made 29 starts for the San Diego Padres, with an ERA of 3.71.

Hensley began the 2007 season as the Padres' #5 starter, but was placed on the disabled list in May.  After struggling in his minor league rehab starts, Hensley was optioned to the Triple-A Portland Beavers.

On August 4, 2007, Hensley gave up Barry Bonds' 755th career home run, which tied Bonds with Hank Aaron for most all-time.
The next day, Hensley was optioned to the minor leagues.

Hensley was non-tendered by the Padres following the 2008 season, making him a free agent.
On July 13, 2003, he was traded to the San Diego Padres for Matt Herges. On April 5, 2005, he was suspended 15 games for testing positive for steroids while pitching in the minor leagues. Later that season, he was called up from the Triple-A Portland Beavers. He emerged as a vital figure in middle relief, not allowing a home run in 47.2 innings.
In 2006, Hensley made 29 starts for the San Diego Padres, with an ERA of 3.71.
Hensley began the 2007 season as the Padres' #5 starter, but was placed on the disabled list in May.  After struggling in his minor league rehab starts, Hensley was optioned to the Triple-A Portland Beavers.
On August 4, 2007, Hensley gave up Barry Bonds' 755th career home run, which tied Bonds with Hank Aaron for most all-time. The next day, Hensley was optioned to the minor leagues.
Hensley was non-tendered by the Padres following the 2008 season, making him a free agent.
Clay Hensley