Krejčí turned professional in 2006–07, playing for the Bruins' American Hockey League affiliate, the Providence Bruins. He played in his first NHL game on 30 January 2007 in a 7–1 loss against the Buffalo Sabres, but suffered a concussion from Buffalo's Adam Mair during his third shift. He recorded just 2:07 minutes of ice time. Krejčí played increasingly with Boston the following season, appearing in 56 NHL games to go with 25 games for Providence. On 19 February 2008, Krejčí was involved in a shootout tie-breaker round, in a Bruins road game against the Carolina Hurricanes, and scored to help the Bruins take the shootout 2–1. Krejčí's shootout tally would not register as his first NHL goal, as shootout goals do not count towards a player's statistical totals. Krejčí scored his first official NHL goal one week later on 26 February against Martin Gerber of the Ottawa Senators, the second Bruins' goal in a 4–0 home shutout. He finished his rookie NHL season with 6 goals and 27 points. During the 2008–09 season, Krejčí scored his first NHL hat-trick on 18 December 2008 against the Toronto Maple Leafs. He registered his first two goals against starter Vesa Toskala and his third against Curtis Joseph in an 8–5 Bruins win. About the midpoint of that season, NESN's play-by-play TV announcer Jack Edwards for televised Bruins games gave Krejčí the nickname "The Matrix", due to his ability to slow down the pace of a game through his skating style and abilities on the ice. Before a game on 2 April 2009, Krejčí was named the winner of the Boston Bruins' 2009 Seventh Player Award. The award is given annually to the player who "goes beyond the call of duty and exceeds all expectations" throughout the course of the season. During the game, Krejčí assisted on a goal by Milan Lucic, the 2008 winner of the Seventh Player Award, in a 2–1 home ice victory over the Ottawa Senators. He completed his second NHL season with a then-career-high 73 points in 82 games to go with a league-high +37 plus-minus rating. On 2 June 2009, he signed a multi-year contract extension with the Bruins, reportedly a three-year contract paying an average of $3.75 million per year. At the beginning of November 2009, Krejčí was noticeably ill; on 5 November 2009, it was confirmed that Krejčí had been diagnosed with the H1N1 virus, which sidelined him for a period of time. On 5 May 2010, during the 2010 Stanley Cup playoffs, Krejčí dislocated his wrist less than five minutes into a game when he was checked at the Bruins' blue line by Philadelphia Flyers' centre Mike Richards. Surgery was needed and was performed following the game at Union Memorial Hospital in Baltimore, and Krejčí missed the remainder of the playoffs. On 25 May 2011, in Game 6 of the Eastern Conference Finals against the Tampa Bay Lightning, Krejčí recorded his second NHL career hat-trick. He was the first Bruin to record a playoff hat-trick since Cam Neely, two decades prior. On 15 June, Krejčí and the Bruins won the team's first Stanley Cup in 39 years after defeating the Vancouver Canucks 4–0 in Game 7 of the Finals. Krejčí finished the 2011 playoffs with a playoff-leading 12 goals, 23 points and 4 game-winning goals. On 1 March 2012, in a game against the New Jersey Devils, Krejčí scored his third career hat-trick, scoring in the first, third and overtime period in a 4–3 win. In Game 4 of the 2013 opening round playoffs against the Toronto Maple Leafs, Krejčí scored a hat-trick, including the game-winning goal in overtime. On 1 October 2013, Krejčí was named an alternate captain of the Bruins. On 25 October 2013, he scored a game-winning goal with 0.8 seconds left against the San Jose Sharks and goaltender Antti Niemi. On 3 September 2014, Krejčí signed a six-year contract extension with the Bruins. During a road game on 20 February 2015 against the St. Louis Blues, Krejčí suffered a partial tear of his MCL in his left knee, forcing him off the ice for 4–6 weeks for a recovery. During the Bruins' home game against the Toronto Maple Leafs on 8 December 2018, Krejčí became the tenth-highest scoring Bruins' player of all-time when he recorded a goal and an assist in a 6–3 Bruins' win, bringing his points total to 592. Three days later, on 11 December, Krejčí played his 800th NHL game, recording three assists in a Bruins' 4–3 home win over the Arizona Coyotes. Just one week later, on 20 December, Krejčí recorded his 600th career NHL point after scoring the Bruins' third goal in a 4–1 home ice defeat of the Anaheim Ducks.