On July 1, 2012, Carkner signed a three-year contract with the New York Islanders. He played with the team during the next two seasons, but a back surgery in the 2014 offseason left him sidelined for the first 56 games of the 2014–15 season. He was activated off of the injured reserve list and placed on waivers on February 15, 2015 and cleared the next day, being assigned to the team's minor league affiliate, the Bridgeport Sound Tigers of the AHL.