He started his career with AGF, before moving to Brøndby, and afterwards abroad to play for Italian club Ancona and Norwegian side Stabæk.
Born in Ryomgård, Jørgensen started his career at local club AGF in the top-flight Danish Superliga championship.
Despite his status as a free agent, he demanded that Brøndby pay AGF DKK 1 million in compensation, before signing a two-year contract in June 2001.
His first time at Brøndby was a success, as he scored ten goals in his first season and helped the club win the 2001–02 Danish Superliga.
At Stabæk, Jørgensen looked to replace Norwegian international midfielder Martin Andresen, and he scored two goals in his debut match; a 3–1 win against Sogndal.
Playing the last half of the 2004–05 season, he helped the club complete the Double in 2005, winning both Superliga and Danish Cup titles that year.