In FC Nordsjælland Junker got off to a flying start, scoring 11 goals in the first half of the season. During the last half, however, he only managed to score twice. His second season got off to a wrong start as Junker was caught red handed cheating his team mates in a series of poker games. In total Junker swindled his team mates out of 100.000–150.000 DKK. 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 a few friendships. As punishment he was replaced as vice-captain by Kim Christensen. After the gambling incident Junker became increasingly modest, always praising team performance instead of personal ability. Whether this had an influence is unknown, but Junker finally found the stability that had been lacking. Citing the 4–4–2 system and his team as a major factor, Junker scored 15 goals in first half of the season, thus once again attracting attention from abroad.
Vitesse
During the winter break, Junker signed with Eredivisie side Vitesse Arnhem for a fee of 10 million DKK as a replacement for Matthew Amoah. He made his debut against Feyenoord, but had to be substituted after an hours play due to a hip injury. Junker scored his first goal in the home game against Heerenveen. In total he managed 9 goals for Vitesse in the second half of the 2004–05 season. During his first season in Vitesse, Junker was asked for advice when Vitesse looked into the possibility of signing his former team mate from FC Nordsjælland, Anders Due. Vitesse signed Due for a fee of 10 million DKK in July 2006. During the beginning of his second season Junker lost his first team spot to Anduele Pryor. Junker, not happy with the situation, spoke to the media about the possibility of leaving the club. During the winter transfer window, Junker was about to sign with FC Utrecht, but Vitesse cancelled the deal on the last day of the transfer window, as the club feared playing with only three strikers for the rest of the season. After the end of the 2006–07 season Utrecht were reportedly still interested, but Vitesse refuse to sell the player who was supposed to have a greater role in the upcoming season.
In July 2010, Junker signed with Roda JC. The season before, he had already played for the club on loan, in which he scored 21 league goals in 34 matches.
Junker made his first appearance for the Danish national team on 16 August 2006 in the friendly against Poland, when he replaced Nicklas Bendtner in the 67' minute. Before this he had played 6 games for the U-21 team, 5 games for the U-20 team and 2 games for the U-19 team.
