Thompson signed an entry-level contract with the Bruins on July 20, 2005, and made his debut in the NHL with the team in 2006–07, playing four games; however, he spent the majority of the season with Providence in the AHL. Just prior to the start of the 2008–09 season, on October 8, 2008, Thompson was claimed off waivers by the New York Islanders. He scored his first career NHL goal against Henrik Lundqvist of the New York Rangers just under one month later, on November 4. On July 27, 2009, Thompson was re-signed to a one-year contract with the Islanders. After registering six points in 39 games with the Islanders in the 2009–10 season, Thompson was claimed off waivers by the Tampa Bay Lightning on January 21, 2010. He would appear in 32 games for the Lightning, scoring one goal and three assists for four points; in total, he scored two goals and eight assists for both the Islanders and Lightning, then-career-highs. He also excelled in face-offs, winning 219 of 385 taken for Tampa Bay, a 56.9 percent success rate. In the subsequent off-season, on July 10, 2010, Tampa Bay re-signed Thompson to a one-year contract. On January 31, 2011, Tampa Bay signed Thompson to a two-year contract extension. At that point, he had played in 51 games with the team, recording career-highs for goals, assists and points. Thompson also continued his success in the face-off circle, winning 249 of 446 draws taken. He ranked seventh among NHL forwards with 49 blocked shots, and was also fourth on the team in takeaways, with 25. During the 2012–13 NHL lockout, Thompson played for his hometown Alaska Aces of the ECHL, later returning to the Lightning at the end of the lockout. On March 3, 2013, Tampa Bay signed Thompson to a four-year contract extension. He finished the shortened, 48-game 2012–13 season with seven goals and eight assists from 45 games played. He played in 81 games during the 2013–14 season, scoring nine goals and seven assists for 16 points. On June 29, 2014, Thompson was traded by Tampa Bay to the Anaheim Ducks in exchange for two picks in the 2015 NHL Entry Draft. In his first season with the Ducks, Thompson appeared in 80 games, scoring five goals along with 13 assists. On December 14, the NHL department of player safety issued a three-game suspension against Thompson for his hit onJustin Faulk of the Carolina Hurricanes. The suspension was deemed an illegal check to the head. Thompson was given a game misconduct at the time of the incident. As a result of the suspension, Thompson lost $25,806.45 in salary. After three seasons with the Ducks, Thompson left as a free agent to be reunited with former Lightning head coach Guy Boucher, in signing a two-year, $3.3 million contract with the Ottawa Senators on July 1, 2017. On February 13, 2018, Thompson was traded to the Los Angeles Kings along with Dion Phaneuf in exchange for Marián Gáborík and Nick Shore. In the 2018–19 season, on February 11, 2019, Thompson was traded to the Montreal Canadiens along with a fifth-round pick in the 2019 NHL Entry Draft for a 2019 fourth-round pick. He played a total of 25 games for the Canadiens, recording one goal and six assists. On April 25, 2019, the Canadiens signed Thompson to a one-year, $1 million contract extension. In a fourth-line center role with the Canadiens in the 2019–20 season, Thompson collected 4 goals and 14 points in 63 games before he was traded to his eighth NHL team, the Philadelphia Flyers, in exchange for a fifth-round pick in 2021 on February 24, 2020.
Personal life
Born a Christian, Thompson decided to begin the conversion process to Judaism before marrying his second wife, Sydney, who is Jewish, and he is now Jewish. On January 11, 2020, a feature aired on Sportsnet in which Thompson sat down with Chris Simpson to discuss his former alcohol and drug addiction.