[3][4] Born in Copenhagen, Junker made his debut in the Danish Superliga in 2000, playing for Lyngby BK while attending High School on the side.

Junker did not fit into the 4–2–3–1 system favoured by Brøndby manager Michael Laudrup and in 2004; he was sold to FC Nordsjælland.

Junker said his desire to win had caused him to use dishonest means, and stated that the incident had taught him a lesson as well as cost him a few friendships.

Citing the 4–4–2 system and his team as a major factor, Junker scored 15 goals in the first half of the season, thus once again attracting attention from abroad.

During the winter break, Junker signed with Eredivisie side Vitesse for a fee of DKK 10 million as a replacement for Matthew Amoah.

In July 2014, Junker signed for the Indian Super League side Delhi Dynamos FC and he wore the No.

Junker made his first appearance for the Danish national team on 16 August 2006 in a friendly against Poland, when he replaced Nicklas Bendtner in the 67' minute.