Drafted 58th overall by the Montreal Canadiens in the 1999 NHL Entry Draft, Carkner never signed with the team and instead joined the San Jose Sharks as a free agent in 2001. He spent time in the Sharks' AHL affiliate before making his NHL debut during the 2005-06 season. Throughout his NHL career, Carkner played for the San Jose Sharks, Ottawa Senators, and New York Islanders, known for his gritty playstyle. His tenure with the Ottawa Senators saw him contributing significantly, particularly during the 2009-10 season when he played in 81 games, registering two goals, 11 points, and 190 penalty minutes. Carkner also made a memorable impact during the playoffs, notably scoring a triple-overtime goal in Game 5 of the Eastern Conference quarter-finals. In 2012, Carkner signed a three-year contract with the New York Islanders, where he played for two seasons before injuries limited his playing time. He officially retired from professional hockey in 2016 and transitioned into coaching, accepting a position as an assistant coach with the Bridgeport Sound Tigers, the Islanders' AHL affiliate.