Boyes made his NHL debut in 2003 for the San Jose Sharks, but only played in one game before returning to the AHL.

Traded to the Buffalo Sabres in 2010, he remained with the team for two seasons before being acquired by the New York Islanders in 2012.

[5] On March 9, 2002 He was traded to the San Jose Sharks along with Alyn McCauley and a 1st-round selection in the 2003 NHL Entry Draft in exchange for Owen Nolan.

[8] Boyes made the Bruins out of training camp for the 2005–06 season and scored his first NHL goal on October 8, 2005, against Sébastien Caron of the Pittsburgh Penguins.

[9][14] He scored his first NHL hat trick on March 18, 2006, against Cam Ward of the Carolina Hurricanes.

[15] He finished the season with 26 goals and 69 points in 82 games and was named to the NHL All-Rookie Team.

On February 27, 2011, Boyes was traded by the Blues to the Buffalo Sabres in exchange for a second-round pick in the 2011 NHL Entry Draft.

[23] During his final season with the Sabres, Boyes became the 20th player in NHL history to play in 500 consecutive games.

[25] On July 1, 2012, Boyes signed as a free agent to a one-year, $1 million deal with the New York Islanders.

[27] Unsigned in the offseason, Boyes was offered a professional try-out contract by the Islanders and the Florida Panthers.

Despite picking up 38 points in 78 games and having good advanced analytics, Boyes was unable to find a deal, and on September 10, 2015, he signed a professional tryout contract to attend training camp with the Toronto Maple Leafs, the team who originally drafted him in 2000.