On 30 March 2017, Danish Superliga club OB announced that Mikkelsen would join the first team on free transfer beginning on 1 July.

[20] After Lyngby suffered relegation to the second tier after the 2020–21 season, Mikkelsen signed with defending Danish champions Brøndby IF, joining them from 1 July 2021.

[21][22] Featuring as the backup to Mads Hermansen, Mikkelsen made his debut in goal on 23 September in a 8–1 win over Allerød FK in the Danish Cup.

[25][26] He would also make his European debut during Hermansen's absence, playing the UEFA Europa League group stage match against Rangers, which ended in a 2–0 loss.

[27] After Hermansen was sold to EFL Championship club Leicester City, Mikkelsen assumed the role of starter early in the 2023–24 season.

[29] However, he eventually lost his starting place when Patrick Pentz joined the team on a season-long loan from Bayer Leverkusen in August 2023.