Jørgensen amassed 102 caps and scored 12 goals for the Denmark national football team. He is the only player that has represented Denmark at three FIFA World Cups. He has also played at two European Championship tournaments. After Denmark's elimination from the 2010 World Cup, Jørgensen announced his retirement from the national team. As he was close to reach his anniversary match no.100 for the national team, the coach Morten Olsen however decided to call him up for one last farewell match, in November 2010. After a brief retirement, he returned to the national team as he was called up for the Euro 2012 qualifying match against Norway on 6 September 2011.