Duchscherer appeared in 53 games out of the bullpen, sporting an ERA of 3.27. In 2005, he was selected to the American League All-Star team, the A's lone representative, but did not pitch in the game. He finished the year with 7 wins out of the bullpen and a 2.21 ERA as the top setup man for rookie closer Huston Street. During the season, Duchscherer spent most of the season on the disabled list with an injured right hip that required season-ending surgery. For the season, Duchscherer returned to the starting rotation for the A's. Duchscherer spent about three weeks on the disabled list with an inflamed biceps in April. After returning to the rotation, Duchscherer was outstanding and, at one point, led the major leagues in ERA. He was selected to the 2008 MLB All Star Game. Duchscherer missed the 2009 season due to shoulder and back injuries and a bout with clinical depression. He became a free agent following the season, rejecting the A's arbitration offer. On December 30, 2009, Duchscherer signed a one-year contract with a base salary of $2 million, with another $3.5 million with incentives with the Oakland Athletics  Duchscherer made 5 starts for Oakland in the first month of the 2010 season, posting a 2–1 record with a 2.89 ERA, but went on the disabled list in May and missed the remainder of the season. He became a free agent on November 2. On January 30, 2011, Duchscherer signed a one-year deal with the Baltimore Orioles. He was released on August 2.