After his second OHL season, Thornton was selected first overall in the 1997 NHL Entry Draft by the Boston Bruins. Thornton suffered a fractured arm in the Bruins' pre-season but made their roster for the 1997–98 campaign. He scored his first career NHL goal on December 3, 1997, in a 3–0 win against the Philadelphia Flyers. Bruins head coach Pat Burns was measured in his deployment of Thornton, using him almost exclusively on the fourth line and making him a regular healthy scratch. Averaging eight minutes and five seconds of ice time per game over the course of the season, he registered three goals and seven points in 55 games as a rookie. In the 1998 Stanley Cup playoffs, Thornton went scoreless in six games.