Jørgensen was called up by Johansson to compete for Denmark at the 2000 European Championship, despite being injured. The tournament was no success for Jørgensen, who played a single game as Denmark were eliminated in the preliminary group stage. He made his second World Cup appearance, under new coach Morten Olsen, at the 2002 FIFA World Cup. He played in Denmark's three group stage matches, before suffering an injury which kept him from playing the 2nd round where Denmark were eliminated. At the 2004 European Championship, Jørgensen played in all Denmark's four matches before elimination.