At the start of the 2009/10 season, Ankergren was Leeds' number two goalkeeper behind Shane Higgs. Ankergren made his first appearance of the season coming on as a substitute for Higgs who suffered an injury during the match against Milton Keynes Dons, opening the door for Ankergren to start a few matches after Higgs was ruled out with a thigh injury. Leeds signed goalkeeper Frank Fielding as backup to Ankergren whilst Higgs was injured. Ankergen made his first start of the season against Carlisle United. He started a second successive match with Higgs still out and he kept a clean sheet in the match against Charlton Athletic. He continued to deputise for the injured Higgs and played 11 matches in all competitions with six clean sheets. New loan signing David Martin came into the team for the Football League Trophy match against Accrington Stanley with Ankergren dropping to the bench, but he returned to the starting line-up against Southampton and kept another clean sheet. With Higgs' injury more serious than originally thought, Ankergren has been given an extended run of matches.