In the summer 2019, Pedersen began working as talent coach for his former club,
HB Køge, helping with the morning- and individual training. On 6 January 2020 the club announced, that he would take charge of the club's U17 squad. On 5 June 2023, after
Daniel Agger resigned, Pedersen was appointed manager of
HB Køge's first team. ==Honours==