He started the 2005–06 season in the Brøndby goal, but at the winter interval, Zaza was once again selected as first choice keeper. However, Zaza left the club in the summer of 2006 and Ankergren signed a new three-year contract. Brøndby had a disappointing start to the 2006–07 season, sitting in seventh place at the winter break. However, Ankergren was called up to the Denmark national team by national manager Morten Olsen in October 2006, where he served as a back-up goalkeeper for Jesper Christiansen. When Brøndby bought former Danish international goalkeeper Stephan Andersen, Ankergren announced his decision to leave the club.