Bergesen was called up to the Baltimore Orioles from the Triple-A Norfolk Tides to make his first major-league start on April 21, 2009. He pitched 5 innings for the win against the Chicago White Sox, allowing three runs on four hits and two walks, striking out four. Bergesen's starts for the next month would be much rockier, as his ERA quickly increased and sat at 5.49 after a start on May 24. Bergesen's year turned around dramatically at this point. From May 29 through July 30, he pitched at least six innings each start and allowed more than three earned runs only once. He had a particularly impressive stretch from May 29 to June 14, when over four starts he pitched 32 innings and allowed just six runs. The start on June 14 was his first career complete game, an 11-2 victory over the Atlanta Braves. Bergesen continued to pitch well over the course of the year, emerging as the Orioles' most dependable starting pitcher as the summer continued. Unfortunately for the Orioles, his final start would be on July 30, against the Kansas City Royals. Bergesen was pitching another solid game, having allowed only one run thus far, and was one out away from getting out of a jam in the seventh inning when the Royals' Billy Butler hit a line drive straight into Bergesen's left shin. Bergesen collapsed immediately upon being hit, and the ball rolled back towards Orioles catcher Matt Wieters, who threw Butler out at first. Bergesen managed to get up quickly, slap gloves with Wieters, and hobble into the Orioles' dugout unassisted before collapsing in the tunnel. X-rays and an MRI did not reveal any bone fracture, but the injury would end Bergesen's season. Bergesen finished the 2009 season with 19 starts, 123 innings pitched, a WHIP of 1.28, and an ERA of 3.43. Many writers have suggested that if Bergesen had continued to pitch as well as he had and had not been injured, he would have been a strong candidate for Rookie of the Year. On April 20, 2010, Bergesen was optioned to Norfolk. On May 14, 2011, Bergesen threw a complete game shutout of the Tampa Bay Rays. Bergesen did not allow a single base hit throughout the last six innings of the game. It was his fourth career complete game, but it was his first complete game shutout of his career. On May 29, 2011, Bergesen was optioned to Triple-A Norfolk, giving up his spot in his rotation to Brian Matusz. In June, he returned to MLB in a relief role in exchange for Jeremy Accardo. Bergesen was designated for assignment on May 12, 2012. He was later re-added to the 40-man roster, but was designated for assignment again on July 18.
Arizona Diamondbacks
On July 20, 2012, he was claimed off waivers by the Arizona Diamondbacks.
Chunichi Dragons
On November 30, 2012, he signed with the Chunichi Dragons of the NPB's Central League. In 14 appearances, Bergesen was 2-2 with a 3.71 ERA, but he posted a meager 3.7 strikeouts per 9 innings.
Brad Bergesen is a finesse pitcher and groundball pitcher who relies primarily on a sinker. He also uses a slider and changeup, the slider being his typical strikeout pitch. Because his fastball averages a speed of about 89 mph, Bergesen relies on good control of his pitches and avoids walks, rather than striking lots of batters out. His ability to get many ground balls helps him limit hits to singles and get extra outs via the double play. Though he still allows many home runs.