The following season, Thornton improved to 41 goals and 122 points, second overall in League scoring behind Marc Savard of the Oshawa Generals, and was named to the OHL Second All-Star Team. 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. In 1998–99, Thornton saw significantly more ice time, averaging 15 minutes and 20 seconds per game, and improved to 41 points in 81 games, as well as a 9-point effort in 11 playoff games. Thornton continued to build into a key player in the Bruins' line-up, increasing his points total in each of the following two campaigns. Prior to the 2002–03 season, he was named team captain, succeeding Jason Allison, who was traded to the Los Angeles Kings in 2001; the captaincy position was vacant for a full season after Allison's departure. In his first season as team captain, Thornton recorded 68 points over 66 games. The following year, he notched his first career 100-point season with 36 goals, a career-high, and 65 assists. He ranked third in NHL point-scoring, behind Peter Forsberg of the Colorado Avalanche and Markus Näslund from the Vancouver Canucks. Thornton's production declined to 73 points in 77 games in the 2003–04 campaign. He suffered a fractured right cheekbone in a fight with New York Rangers centre Eric Lindros during a game on January 19, 2004. The two power forwards fought after Lindros cross-checked Thornton in the head. The injury required surgery, keeping him out of the line-up for three games. The 2003–04 campaign also saw a drop in Thornton's goal-scoring production that has never since rebounded; his last 30-goal season came during the 2002–03 season. In 2003–04, Thornton's production decreased to 73 points over 77 games. During the 2004–05 NHL lock-out, Thornton went abroad to play for HC Davos of the Swiss National League A (NLA).