Baker was expected to be the Twins' Opening Day starter, but he opened the 2009 season on the disabled list with right shoulder stiffness and posted a 9.15 ERA in his first four starts when he returned. On May 3, he no-hit the Royals through six innings, but he gave up five runs in the seventh inning of that game. He earned his first win on May 8, pitching seven shutout innings in an 11–0 victory over the Seattle Mariners. On May 24, he gave up three runs in innings and earned the win in a 6–3 victory over Milwaukee. Baker began trying to stand taller in his delivery, and on June 4 he struck out a career-high 10 batters in an 11–3 victory over the Indians. Baker went 4–0 in June, and from July 12 through September 5, he set a career-high with seven straight wins. On August 14, he had a two-hit shutout in an 11–0 win over Cleveland. After sitting seven games out of the AL Central lead on September 6, the Twins forced a tiebreaker with the Tigers, and Baker made the start. He allowed three runs over six innings, left eligible for the win, but took a no-decision. However, the Twins won 6–5 in 12 innings to clinch a trip to the playoffs. He led the Twins with 15 wins, 162 strikeouts, and finished second on the team behind Nick Blackburn with a 4.37 ERA, while pitching a career high 200 innings. However, the Twins were swept in three games in the AL Division Series (ALDS) against the Yankees, preventing Baker from making any playoff appearances.