He was later put in charge of the Denmark national under-21 team, before being appointed head coach of Brøndby in June 2019, replacing Alexander Zorniger.

[5][1][6] Frederiksen has cited his main influences inside football as José Mourinho "for his arrogance", Sir Alex Ferguson "for his long time success" and Jürgen Klopp, due to his development of young players and his tactics.

[12] He continued coaching the first team during the 2009–10 season while managing an HR unit within Danske Bank where he had also become chief operating officer.

[19] By 1 September 2011, Frederiksen was released from his employment obligations in the Danske Bank Group, and the following week he was appointed manager of Lyngby, where he was also put in charge of transfers.

[21] On 2 May 2013, Esbjerg fB announced that Frederiksen would succeed Jess Thorup as the club's head coach from the start of the 2013–14 Danish Superliga season.

[29] In the domestic league, Esbjerg had sold some profiles such as Jakob Ankersen, Eddi Gomes and Martin Pušić during the winter transfer window,[30][31][32] and partly due to this the club struggled against relegation.

Frederiksen's defense consisted of Hjörtur Hermannsson, Andreas Maxsø and Sigurd Rosted, which neutralised Copenhagen-strikers Nicklas Bendtner and Michael Santos.

[43] After winning the subsequent league match 3-0 over Frederiksen's former club, Lyngby, he stated that the 3-5-2 was a system suited for his team's abilities.

The altering of the first-team meant that talents such as Morten Frendrup and Anis Ben Slimane began to play a larger role for the club in the spring of 2020.

[45][46] Frederiksen had a strong start to the 2020–21 season with Brøndby, who won the first four matches including stoppage time wins over Nordsjælland and main rivals FC Copenhagen.

[47] At the winter break, the team were in joint first place of the league table alongside Midtjylland, but had been knocked out of the cup by second tier club Fremad Amager.

[52] Due to Brøndby's poor performance in the first half of the 2022–23 season, Frederiksen was dismissed on 14 November 2022, the day following the final game before the winter break, a 2–0 loss to Viborg.

[53] On 14 May 2024, it was announced Frederiksen would take on his first managerial job abroad, when Polish Ekstraklasa club Lech Poznań revealed him as their new manager, starting from 1 July.

[21] Frederiksen has a master's degree in economics from University of Southern Denmark,[55] and worked in Danske Bank for several years, while having a part-time job as youth coach at B.93 and Lyngby Boldklub.