While at Manchester City, Ellegaard served as a stand-in for Thomas Sørensen in the initial Denmark national team training sessions ahead of the 2004 European Championship. He was not a part of the Danish squad at the tournament. In the fall of 2007, while playing for Randers, Ellegaard was called up as the Danish third choice goalkeeper due to the injury of Jesper Christiansen. In August 2008, Ellegaard was called up for the national team again, due to a new Jesper Christiansen injury.