In his first seven starts, he lasted six innings or more six times, and allowed two earned runs or less six times. On May 11, he threw five no-hit innings, then took himself out because of elbow soreness, ending up on the 15-day disabled list. He returned on August 14 in a start against the Phillies. He pitched six innings of one-hit ball, while striking out seven and walking only one. Hill's 2008 season was cut short due to injury. He was placed on the disabled list twice for arm problems before his season was ended on June 25, 2008. Hill underwent arthroscopic surgery to remove bone spurs on his right elbow in September 2008. During the 2008 offseason, he went to an arbitration hearing with the Nationals, winning the case. Washington paid him $775,000 in 2009, instead of the $500,000 they had offered. On March 18, 2009, Shawn Hill was released by the Washington Nationals. Hill signed a minor league contract with the San Diego Padres on March 23, 2009. Hill managed to pitch in just 3 starts for the Padres. On June 24, 2009, Hill had his second Tommy John surgery. On October 8, he was released by the Padres. On January 22, 2010, Hill signed a minor league contract with the Toronto Blue Jays, with an invitation to spring training. Hill spent most of his 2010 season in the minor leagues with the Blue Jays organization, and pitched very well at all stops, the last of which was the Las Vegas 51s, the Jays' Triple-A team. Hill posted a 1.61 ERA in 11 minor league starts in 2010. On September 6, 2010, Hill was called up to the Toronto Blue Jays. He started on September 9 against the Texas Rangers, in his first major league action in more than 26 months. Hill lasted 5 innings, allowed three earned runs, and was given the loss in a 4–2 game. Hill finished the season compiling a 1–2 record in four starts with a 2.61 ERA and 14 strikeouts in 20 innings pitched. On November 15, 2010, Hill was released by the Blue Jays. On January 29, 2011, Hill signed a minor league contract with the Florida Marlins with an invitation to Spring training. Hill went on to pitch in just 4 games in Spring training before being released. He did not pitch for any organization in 2011 following his release. On June 18, 2012, the Blue Jays signed Shawn Hill to a minor league contract. On October 4, he was outrighted to the Blue Jays' Triple-A affiliate Buffalo Bisons.