Bergeron was drafted in the 2003 NHL Entry Draft by the Boston Bruins 45th overall. During his rookie season, Bergeron was selected for the All-Star Weekend NHL Young Stars game in Minnesota.

 

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 5 goals and 8 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.

 

In his second season, Bergeron, only 20 years old, led the Bruins with 31 goals and 73 points, and finished second on the team with 42 assists. Following the season, he again played for Canada at the Senior Men's World Championships, finishing 2nd to teammate Sidney Crosby in tournament scoring with 14 points.

 

Bergeron was once again invited to play for Canada in the World Championships. He declined, citing that he wanted to recover and avoid any future injuries.