Brøndby IF Agger started playing youth football with Brøndby IF, and was included in various Danish national youth teams, making his debut for the Denmark under-17 team in August 2004. Playing in the Brøndby reserve team, he made his senior debut for Brøndby IF in August 2006, replacing
Morten "Duncan" Rasmussen and scoring two goals in the 4–0 victory over
FC Flora Tallinn in the second qualification round of the
UEFA Cup, after being subbed on in the beginning of the second half. Agger made his
Danish Superliga debut in an October 2006 matchup against
AaB. In the summer of 2007, Agger was officially promoted to the first team squad. He made nine league appearances for Brøndby in his first two seasons.
Loan to SønderjyskE On 2 September 2009 it was announced, that
SønderjyskE had signed Agger a 4-month loan deal. In November 2009, Agger broke his ankle in a match against
HB Køge and was ruled out for six months. While Agger was loaned out to
SønderjyskE, Brøndby would extend his contract until December 2013. On 20 May 2011, he scored two goals against
Lyngby Boldklub in a
Danish Superliga game. After his return from a loan spell at SønderjyskE, Agger became a regular part of the Brøndby squad and played 26 league games in the
2012–13 season. However, during the season, he received less and less playing time, and he would eventually leave the club on loan once again.
Loan to Djurgårdens IF On 31 August 2011, Agger joined Swedish club
Djurgårdens IF on loan to the end of the season with a buying obligation. Agger scored in his debut against Trelleborg, a match which his team would win 4–3. Djurgårdens did not trigger his release clause, and he returned to Brøndby after seven league appearances for Djurgården. After his loan spell at
Djurgårdens IF, Agger stated, that he was not interested in another loan. Either he would play for Brøndby, otherwise he would be leaving the club.
Vejle On 6 August 2012 Agger moved to
Vejle-Kolding on a 3-year deal. In his second season at the club, he was mostly used on the left wing position.
Silkeborg On 29 June 2014,
Vejle Boldklub announced that Agger had been sold to newly promoted
Silkeborg IF a year before the end of his contract. Vejle later revealed, that they had to sell him in order to acquire other players. In October 2016, Agger suffered an anterior cruciate ligament injury to his left knee, which would rule him out for six months. Agger announced in May 2017, that he would leave the club after three seasons, when his contract expired in the summer. He also announced, that he probably would stay in Denmark.
Hvidovre IF On 25 July 2017, Agger signed for
Danish 2nd Division and hometown club
Hvidovre IF. He reached promotion to the
Danish 1st Division in his first season with Hvidovre, scoring 19 goals in 27 league appearances. On 30 June 2021, 32-year old Agger announced his retirement from football. ==International career==