Allen was the 4th overall choice in the 1998 NHL Entry Draft to the Vancouver Canucks. A big, bruising defender with a mean streak, Allen earned comparisons to Derian Hatcher at the time of his selection.
Allen made the Canucks at the age of 18 in his first camp, but was unable to reach an agreement with the team's management and returned to the Oshawa Generals, his junior team. Despite being limited to 37 out of his team's 66 games, his strong leadership style of play earned him OHL First All-Star Team honours. He was also selected to represent Canada at the 1999 World Junior Championships.
After missing substantial parts of the two previous seasons due to injury, he missed virtually all of the 1999–00 campaign following surgery.
Allen would play most of his first two professional seasons in minor-pro before earning a regular roster spot in the 2002–03 season, appearing in 48 games and scoring 5 goals. With the departure of Murray Baron in the summer of 2003, Allen became a regular for the Canucks, and did a fine job of replacing Baron's size and physical play. He was especially a standout on the penalty kill, logging heavy minutes as the Canucks finished near the top of the league in that category. On November 5, Allen was suspended for two games following an incident on November 3 in which he slashed Detroit Red Wings forward Henrik Zetterberg's leg, breaking it.
During the 2004–05 NHL lockout, Allen suited up for Khimik Voskresensk of the Russian Superleague to stay in game shape. Back in Vancouver for the 2005–06 season, with the departures of Marek Malik and Brent Sopel, as well as long-term injuries to several other defenders, Allen's icetime skyrocketed and he became one of the team's most important defenders, finishing with career highs of 7 goals and 17 points.
On June 23, 2006, Allen was involved in a multi-player trade that sent him, Todd Bertuzzi, and Alex Auld to Florida in exchange for Roberto Luongo, Lukas Krajicek and a 6th round draft pick. The 2006–07 season would be the best of his career to date, as he set career highs with 21 assists and 25 points and established himself as one of the Panthers' top defenders.
A knee injury caused Allen to miss all but two games of the 2008–09 season with the Panthers.
On February 28, 2011, Allen was traded by the Panthers to the Carolina Hurricanes for forward Sergei Samsonov.
On July 1, 2012 Allen signed a three-year contract as a free agent with the Anaheim Ducks. On November 20, 2014 during the 2014–15 season, the final year of his contract, Allen was traded by the Ducks to the Montreal Canadiens in exchange for forward Rene Bourque.
Allen represented Canada at the 1999 World Junior Championships. He recorded one goal and three points in 7 games to help Canada to a silver medal. His goal was a huge one, the tying goal late in the final against Russia, but Russia would ultimately win in overtime.
Allen was expected to be a leader for Canada at the 2000 World Junior Championships, but was unable to play as he was recovering from injury.