After initially working as character animator at Sullivan Bluth Studios under the direction of Don Bluth, he joined Danish animation studio A.
After a period as the creative head of Feature Animation, also acting as sequence director on several films, he went on to co-direct (with Stefan Fjeldmark) the 2006 film Asterix and the Vikings, based on René Goscinny and Albert Uderzo's comic book.
In March 2008, Jesper Møller founded Copenhagen-based independent movie company Parka Pictures ApS.
In 2011, Jesper Møller was nominated "Director of the Year" at the Cartoon Movie 2011 in Lyon – France, for Sandman and the Lost Sand of Dreams.
1988–1990: Animator on All Dogs Go to Heaven, Rock-a-Doodle and A Troll in Central Park.