A feisty player who enjoys the physical game, Thornton played two seasons in Peterborough before joining the AHL's St. John's Maple Leafs in 1997-98. The Oshawa, Ontario native spent four seasons with the Baby Leafs racking up over 1,200 minutes in penalties before having his rights dealt to the Chicago Blackhawks in the summer of 2001.

Upon his arrival with the Blackhawk organization the former Peterborough Pete spent the majority of his playing time with the AHL's Norfolk Admirals while seeing limited action with the parent club.

After his stint with the Blackhawk organization Thornton was signed as a free agent by the Anaheim Ducks on July 14, 2006. Thornton would appear in 48 regular season games with the Ducks that season, recording two goals, seven assists, and 88 penalty minutes. He also saw action in 15 of the Ducks' 21 playoff games en route to the club's first every Stanley Cup championship.

In the summer of 2007, Thornton became a free agent and opted to sign with the Boston Bruins on July 1, 2007.

In Boston, Thornton would take on all comers, establishing himself as one of the league's most feared tough guys. He also worked on the rest of his game, becoming a solid fourth line player that could be trusted to do more than just fight.

During the 2011 playoffs, Thornton helped the Bruins to the club's first Stanley Cup championship since 1972. After surviving a first round scare from the Montreal Canadiens, the Bruins steamrolled over the Philadelphia Flyers and endured a seven game battle with the Tampa Bay Lightning en route to the Stanley Cup Final where they would take on the powerful Vancouver Canucks.

The Bruins would defeat the Canucks in a seven game classic, with Thornton setting the tone physically on numerous occasions. The win marked the second time the tough guy had hoisted Lord Stanley's mug in five seasons.