From 2006 to 2014, Flick was the assistant coach of the German national team under Joachim Löw, contributing to their victory at the 2014 FIFA World Cup.

Having rejoined Bayern Munich as an assistant coach in 2019, Flick was made interim manager following the departure of Niko Kovač in November 2019.

He was later appointed permanently, and won the UEFA Champions League that season, completing the club's second continental treble.

[6] Flick's managerial career began in 1996 as a player-manager of Viktoria Bammental, which was playing in the Oberliga Baden-Württemberg at that time.

[5] In July 2000, Flick became a manager of the Oberliga Baden-Württemberg side TSG Hoffenheim, winning the league and gaining promotion to the Regionalliga Süd in his first season at the club.

[7][8] Flick later worked briefly as an assistant of Giovanni Trapattoni and Lothar Matthäus and sporting coordinator at Red Bull Salzburg.

[13] On 2 July 2019, Flick joined Bundesliga club Bayern Munich as an assistant coach, under the management of Niko Kovač.

[17] After a satisfying spell as interim coach, Bayern announced on 22 December 2019 that Flick would remain manager until the end of season.

[19] During the 2019–20 season, Flick successfully guided Bayern to win the Bundesliga, DFB-Pokal and UEFA Champions League, thus completing the continental treble for the second time in the club's history.

During his tenure, Bayern lost just seven games and won seven trophies (Bundesliga twice, DFB-Pokal, Champions League, DFL-Supercup, UEFA Supercup, Club World Cup).

[26] On 25 May 2021, the German Football Association announced that Flick signed a three-year contract from 1 August 2021 to serve as the manager of the Germany national team, and he replaced his former boss Joachim Löw after UEFA Euro 2020.

On 4 June 2022, Germany drew 1–1 with Italy in the 2022–23 UEFA Nations League A, and thus became the third coach to stay undefeated in his first ten matches, after Sepp Herberger and Jupp Derwall.

[39] On 23 October, Flick managed a win against his former team Bayern Munich where Barcelona won 4–1 at the Estadi Olímpic Lluís Companys.

[41] While in charge of Bayern Munich, Flick developed the name 'Flicki-Flaka' in the media to characterize the mixed gegenpressing and possession based style of football the team played.

[42] Flick consistently deployed a 4–2–3–1 formation at Bayern Munich featuring a high defensive line that encourages their double pivot and full-backs to adopt positions where they can press the ball as it approaches the midfield third, and to screen and block against switches of play.