Aalborg Boldspilklub
Born in part of Frederikshavn called Abildgård, Møller played with local team Aalborg Boldspilklub (AaB). He got his breakthrough in the top-flight Danish championship, when he was handed his debut by AaB manager Poul Erik Andreasen in 1990. He was called up for the Danish under-21 national team in November 1990, and went on to score 16 goals in 22 games for the under-21 national team, including games at the 1992 Summer Olympics. He made his Danish national team debut in September 1991, under national manager Richard Møller Nielsen, but would spend the following years mainly as a substitute.