B.93 Frederiksen started coaching at age 20, coaching youth teams at
B 1913 in his hometown
Odense. Frederiksen's arrived in
B.93 from
Østerbro,
Copenhagen in 1997, where he was put in charge of some youth divisions. Between 2000 and 2002, he was appointed coach of the under-16 team and followed the players as coach when these reached the under-18 team in 2003–04. In 2005, Frederiksen was put in charge of the entire youth department of B.93, while he also worked as assistant coach to the first team which competed in the
Danish 2nd Division (third highest division). In November 2005, he signed a contract as under-19 coach for
Lyngby Boldklub, and he left B.93 in late 2005.
Lyngby Frederiksen began coaching the
Lyngby Boldklub under-17 and under-19 sides beginning 1 January 2006. During his first season, he led the under-19 team to a second place in the table in the national championship, while they reached third place in 2007. In February 2008, Frederiksen was promoted to the position of head of talent in Lyngby – the club's first since 2004 where
Birger Jørgensen held the position. He also joined the board of the Lyngby Boldklub
aktieselskab. Lyngby ended the
2008–09 season in sixth place, 21 and 19 points, respectively, behind
Herfølge Boldklub and
Silkeborg IF who reached promotion. 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. Frederiksen and Lyngby Boldklub reached promotion during that season, after reaching second place in the table, only behind
AC Horsens and ahead of
FC Fredericia in third place. After reaching promotion to the Superliga, Frederiksen signed a one-year contract extension with Lyngby on 1 July 2010. While working as head coach at the highest level, he took leave as COO in Danske Bank and would only do
consulting assignments. During the
2010–11 season, Lyngby was engaged in a relegation battle but managed to avoid this in the final fixture of the season, on 29 May 2011 in a 2–0 home win over
OB. The club ended in eighth place in the league table. In early June 2011, Frederiksen became a full-time permanent employee in Lyngby. This happened after he signed a three-year contract extension, keeping him part of the club until June 2014. 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. The same year, he received his
UEFA Pro Licence. In his first season, he led Esbjerg to the round of 32 in the
Europa League, where they lost 2–4 over two legs to Italian side
Fiorentina. This came after advancing from the group stage in second place by beating
Standard Liège (2–1; 2–1) and
Elfsborg (2–1; 1–0), and losing two matches to group winners,
Red Bull Salzburg (1–2; 0–3). Esbjerg had qualified to the group stage after winning 5–3 on aggregate over French club
Saint-Étienne. In the following season, Esbjerg knocked out Kazakh side
Kairat Almaty 2–1 on aggregate in the second qualifying round, before facing Polish club
Ruch Chorzów in the third round. In the first leg, Esbjerg drew 0–0 away. However in the second leg, a last-minute goal by
Łukasz Surma for Ruch Chorzów to make it 2–2 to win on away goals, ended Esbjerg's hopes of advancing in the tournament. In the domestic league, Esbjerg had sold some profiles such as
Jakob Ankersen,
Eddi Gomes and
Martin Pušić during the winter transfer window, and partly due to this the club struggled against relegation. In the last fixture of the season, Esbjerg avoided relegation after a 2–1 win over relegation rivals,
FC Vestsjælland. On 10 August 2015, Frederiksen was dismissed by Esbjerg with the side placed last in the Danish Superliga table after four matches into the
2015–16 season, with chairman Søren Poulsen citing "lacking" domestic results as the reason behind the dismissal. Frederiksen was succeeded by
Jonas Dal.
Denmark U21 In August 2015, Frederiksen was named manager of the
Denmark under-21 team, signing a two-year contract. In his first game in charge, they lost 1–2 to
Germany in a
friendly at
Stadion Lohmühle in
Lübeck,
Schleswig-Holstein. Under Frederiksen, Denmark qualified for the
UEFA European Under-21 Championship in
2017 and
2019, where they were knocked out in the group stages, finishing third and second, respectively.
Brøndby Frederiksen returned to club management at the beginning of the
2019–20 season with
Brøndby IF, when the club announced him as their new head coach on 1 June. However, Frederiksen would have to lead the
Denmark under-21 team through the
2019 UEFA European Under-21 Championship before starting in his new position. In Brøndby, he had a mixed start and the club suffered a string of poor results in September. This saw him change the formation from a
4–3–3 to a
3–5–2 in early October, which resulted in a derby win over
FC Copenhagen. Frederiksen's defense consisted of
Hjörtur Hermannsson,
Andreas Maxsø and
Sigurd Rosted, which neutralised Copenhagen-strikers
Nicklas Bendtner and
Michael Santos. 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. In January 2020,
sporting director Carsten V. Jensen sold key players
Kamil Wilczek and
Dominik Kaiser to
Göztepe and
Hannover 96, respectively, which brought forward Frederiksen's key strengths; the development of young players. 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. 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. 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. With Frederiksen's contract expiring in June 2021, speculation arose on his contractual situation and whether his contract would be extended or not. He led Brøndby to their first league title in 16 years, after beating
Nordsjælland 2–0 on 24 May 2021, to secure the club's 11th championship.
Lech Poznań 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. He signed a two-year contract and replaced
Mariusz Rumak at the start of the
2024–25 campaign. Frederiksen's first six months in Poznań saw Lech enter the winter break as leaders, with a three-point advantage over
Raków Częstochowa, but also an early
Polish Cup exit after a first round loss to
third-tier side
Resovia. On 24 May 2025, Lech won 1–0 at home against
Piast Gliwice to clinch their ninth league title. Two days later, Frederiksen was named the Ekstraklasa
Coach of the Season. Lech strengthened their side in the summer of 2025, with the signings of last season's Ekstraklasa Defender of the Season
Mateusz Skrzypczak, winger
Luis Palma and striker
Yannick Agnero, among others, but also lost key figures such as
Patrik Wålemark,
Ali Gholizadeh and
Radosław Murawski to long-term injuries. Lech's
2025–26 campaign kicked off with losing the
2025 Polish Super Cup at home to
Legia Warsaw on 13 July. After winning 8–1 on aggregate against Icelandic side
Breiðablik, and losing the following match-ups against
Red Star Belgrade and
Genk, Frederiksen's Lech entered the
UEFA Conference League league phase. On 3 October, Frederiksen oversaw Lech's 4–1 home victory over Austrian side
Rapid Wien. This win was however followed by two away losses, a 1–2 defeat to
Lincoln Red Imps from Gibraltar and a 2–3 loss to Spanish side
Rayo Vallecano, despite leading the latter game 2–0 at half-time. Lech finished the league phase in 11th and entered the knockout phase play-offs. After eliminating
KuPS, Lech ended their European campaign in the round of 16 after losing 3–4 on aggregate to Ukrainian side
Shakhtar Donetsk. ==Manager profile==