Despite a fifteen-point improvement from the previous season, the Bruins missed the playoffs in 2000-01. Leading scorer Jason Allison led the Bruins.
The following season, 2001-02, the Bruins improved again with another thirteen points, winning their first Northeast Division title since 1993 with a core built around Joe Thornton, Sergei Samsonov, Brian Rolston, Bill Guerin, and the newly acquired Glen Murray. Their regular season success didn't translate to the postseason, as they lost in six games to the underdog eighth-place Canadiens in the first round.
The 2002-03 season found the Bruins platooning their goaltending staff between Steve Shields and John Grahame for most of the season. A mid-season trade brought in veteran Jeff Hackett. The Bruins managed to finish seventh in the East, but lost to the eventual Stanley Cup Champion New Jersey Devils in five games.
In 2003-04, the Bruins began the season with ex-Toronto Maple Leaf goalie Felix Potvin. Later in the season, the Bruins put rookie Andrew Raycroft into the starting role. Raycroft eventually won the Calder Award that season. The Bruins went on to win another division title and appeared to get past the first round for the first time in five years with a 3-1 series lead on the rival Canadiens. The Canadiens rallied back, however, to win three straight games, upsetting the Bruins.
The 2004-05 NHL season was wiped out by a lockout, and the Bruins had a lot of space within the new salary cap implemented for 2005-06. Bruins management eschewed younger free agents in favor of older veterans such as Alexei Zhamnov and Brian Leetch. The newcomers were oft-injured, and by the end of November, the Bruins team traded their captain and franchise player, Joe Thornton (who went on to win the Art Ross and Hart Trophies). In exchange, the Bruins received Marco Sturm, Brad Stuart and Wayne Primeau from the San Jose Sharks.
After losing ten of eleven games before the trade (while the Sharks won Thornton's first seven games in San Jose), the Bruins came back with a 3-0 victory over the league-leading Ottawa Senators, as rookie goaltender Hannu Toivonen earned his first career NHL shutout victory. When Toivonen went down (for the rest of the season) with an injury in January, journeyman goalie Tim Thomas started sixteen straight games and brought the Bruins back into the playoff run. Two points out of eighth place at the Winter Olympic break, the Bruins fired general manager Mike O'Connell in March and the Bruins missed the playoffs for the first time in five years. They finished thirteenth in the Eastern Conference and earned the fifth pick in the NHL Draft Lottery, which they used to draft U.S. college player Phil Kessel, who dropped out of college early to sign with the team on August 17, 2006.
Peter Chiarelli was hired as the new GM of the team. Head coach Mike Sullivan was fired and Dave Lewis, former coach of the Detroit Red Wings, was hired to replace him while Marc Habscheid and Doug Houda were named associate coaches. The Bruins signed Zdeno Chara, one of the most coveted defensemen in the NHL and a former NHL All-Star, from the Senators, and Marc Savard, who finished just three points short of a 100-point season in '05-'06 with the Atlanta Thrashers, to long-term deals. Bergeron was re-signed by the Bruins on August 22, 2006, to a multi-year contract, keeping the developing player on the team for some years to come.
The 2006-07 season ended in the team finishing in last place in the division. The Bruins traded Brad Stuart and Wayne Primeau to the Calgary Flames for Andrew Ference and forward Chuck Kobasew.
In the 2007 off-season, the Bruins acquired Finnish professional goaltender Tuukka Rask on May 5, 2007. Rask had previously been the property of the Toronto Maple Leafs, but his NHL rights were acquired by the Bruins as a result of the deal that sent Andrew Raycroft to the Maple Leafs on June 24, 2006.
After a very disappointing season in which the Bruins played with little passion and the coaching staff showed very little themselves, a shakeup occurred. On June 15 Dave Lewis was fired along with Marc Habscheid (who devised the power play set up). Only Marc Habscheid is staying on with the organization but in different roles. Dave Lewis was hired to be an assistant Coach with the Los Angeles Kings. Peter Chiarelli has said that he didn't like the inconsistent play of the team which played a part in the firings. The Bruins officially announced, on June 21, 2007 that Claude Julien, who was fired late in the 2006-07 season from the New Jersey Devils, has been named as the new Bruins head coach. On August 1, 2007, the Bruins hired Craig Ramsay and Geoff Ward as assistant coaches.
The Bruins also unveiled a new logo basically using a serifed letter "B" for the first time since the 1935-36 NHL season, and a brand new shoulder patch, closely based on the main jersey logo used until the 1931-32 NHL season. Unlike the other NHL teams, the Bruins did not do radical changes from their previous designs. Their new uniform design combines several features of many past Bruins uniforms, substituting the new logo, and adding an NHL logo just below the neck opening.
On June 22, 2007, the NHL entry draft took place, which had been called 'not as deep' as previous years; many experts said that none of the draft-eligible players would be playing in the NHL next year, and that the players would need some development time. The Bruins had the 8th overall pick in the draft, and selected Zach Hamill of the Western Hockey League's Everett Silvertips in the first round. On August 8, 2007, the Bruins signed Hamill to an entry-level contract but will rejoin his junior team for the 2007-08 season.
On September 18, 2007, the Johnstown Chiefs of the ECHL announced they had entered an affiliation agreement with the Bruins for the 07-08 season.