Bergeron was drafted in the 2003 NHL Entry Draft by the Boston Bruins 45th overall. He would go on to play with the Bruins in the following season, scoring 39 points in 71 games. Bergeron was in contention for the Calder Trophy and was dealt a heavy blow late in the season missing 11 games to a shoulder injury. Fellow Boston rookie teammate Andrew Raycroft ended up taking home the trophy. Both Raycroft and Bergeron were selected for the All-Star Weekend NHL Young Stars game in Minnesota, where they were defeated by the Western Conference team.

At the end of the season, Bergeron was selected to play for the Canadian Senior Men's team to compete in Prague at the World Championships, where they won the gold medal. During the 2004-05 NHL lockout, Bergeron played for the Providence Bruins of the American Hockey League before heading to North Dakota to play for the Canadian Under-20 team at the 2005 World Junior Ice Hockey Championships. He finished the tournament with 8 goals and 5 assists totalling 13 points over 6 games. He scored a goal in Canada's 6-1 Gold Medal victory over Russia. Bergeron finished the tournament as its leading scorer, MVP (Most Valuable Player) and All-Star team honours. Bergeron is also the first player to win a Senior Men's Gold Medal before winning a Junior one.

After the Joe Thornton trade on November 30, 2005, which brought Marco Sturm, Brad Stuart, and Wayne Primeau to Boston from the San Jose Sharks, Bergeron stepped in to the role and became a leader for the Bruins. Centering Brad Boyes, a rookie, and Marco Sturm, 26, the first line offense produced most of the Bruins offensive production for that disappointing season. Bergeron, only 20 years old, finished the year leading the Bruins with goals, 31, assists, 41, and points, 72 for the entire year. He finished with a plus-3 rating for the season.