Mikkelsen made his professional debut as part of AGF on 25 July 2004 in a 2–2 away draw against FC Nordsjælland, coming on as an 81st-minute substitute for Jeffrey Aubynn.
[6] He left Fredericia in June 2020, and signed with Aarhus Fremad in the Danish 2nd Division, where he would become a player-assistant to head coach Morten Dahm Kjærgaard.
[7][8] He retired as a player in July 2021 to focus full-time on his role as assistant coach of Aarhus Fremad.
[9] On 14 June 2022 Mikkelsen confirmed, that he accepted an offer to become the manager of Aarhus Fremad's reserve team, which was playing in the Denmark Series.
In July 2023, Mikkelsen joined Odder IGF as assistant coach to Jacob Eichner.