Ankergren started his career with Køge BK in the Danish 1st Division, whom he represented at various Danish national youth teams.
In January 2001, he moved to Danish Superliga club Brøndby IF making his debut in October 2001.
Ankergren got his breakthrough with Brøndby following the retirement of club legend Mogens Krogh in December 2002.
He played the second half of the 2002-03 season, and helped the club win the 2003 Danish Cup.
For the 2003-04 season, Brøndby bought Karim Zaza as their first choice keeper and Ankergren spent the season as a substitute.
At the start of the 2004-05 season, Zaza suffered an injury and Ankergren went on to play the entire season as Brøndby's starting goalkeeper, even after Zaza had recovered.
Ankergren finished the season setting a league record 18 clean sheets in his 32 games in goal, and helped Brøndby win the Double of both the 2004-05 Superliga and 2005 Danish Cup titles.
He started the 2005-06 season in goal, but after the winter interval, Zaza was once again promoted to first choice.
Zaza left the club in the summer 2006, and Ankergren signed a new three-year contract.
Despite Brøndby's disappointing start of the 2006-07 season, Ankergren was called up for the Danish national team in October 2006, serving as backup goalkeeper to number one Jesper Christiansen.
When Brøndby bought former Danish national team goalkeeper Stephan Andersen in the January 2007 transfer window, Ankergren announced his decision to leave the club.