Coming through the youth ranks of Thisted FC playing in the Danish 1st Division, he signed a professional contract with the club on his birthday in 2009.
He was in the starting lineup against FC Sydvest 05 in a Danish Cup game, but had to leave the pitch after only 30 minutes due to an ankle injury.
[6] In the summer transfer window of 2012, Esbjerg fB loaned Kenneth Fabricius from SønderjyskE and therefore, Agger became surplus.
[13] On June 5, 2024, 31-year-old Agger confirmed that he was ending his football career so he could be there for his son, who suffered from an incredibly rare genetic disease.
[14] Mikkel is the older brother of professional footballer Mads Agger,[15] who currently plays for Sønderjyske in the Danish Superliga.