[9] Jørgensen moved to AGF as a youngster in 1989,[10] where his footballing talent was recognized as he was chosen to represent various Danish youth national teams from 1991 onward.

He made his senior debut for AGF on 8 May 1994 in a match against Silkeborg IF,[11] and was a part of the team that won the 1996 Danish Cup trophy.

Jørgensen's contract with AGF had a release clause, permitting him to leave the club on a free transfer in April 1997.

[14] He had important contributions for Fiorentina during that season, scoring two goals in the UEFA Cup fixture against IF Elfsborg,[15] and being a key part of the 3–2 win over Juventus on 2 March 2008.

[12] Jørgensen scored a crucial 90th-minute equalizer against Lecce which secured Fiorentina the fourth and final Champions League slot.

On the second last day of the transfer window, 31 January 2010, Jørgensen returned to his childhood club, Danish AGF for an undisclosed fee.

He took part in all five Denmark matches at the tournament and scored the opening goal in the 3–2 quarter-final defeat to eventual runners-up Brazil.

The tournament was no success for Jørgensen, who played a single game as Denmark were eliminated in the preliminary group stage.

[25] In the summer of 2015, however, his role at AGF changed from U14 coach to scout, while he continued as assistant manager in the national team.