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Flick, who was knocked out of the Champions League on Tuesday night by PSG, had a contract until the end of the 2022/23 season but has asked to have his deal terminated early.
The Bayern boss, who has reportedly fallen out with sporting director Hasan Salihamidzic, confirmed the news on Saturday, saying, "I want to terminate my contract this summer, that is a fact.
"It was important to me that the team finds out about it from me personally. I already told the people in charge after our Champions League elimination during the week.
"I also want to thank the club that gave me the chance to manage this incredible team."
The current European champions, whose defence was ended by PSG despite a win in the second leg earlier in the week, had just taken a seven point lead at the top of the Bundesliga.
RB Leipzig's 0-0 draw with Hoffenheim on Friday but Bayern in a great position, and they made it even better as Jamal Musiala scored twice, and Eric Choupo-Moting scored once, in a 3-2 win over Wolfsburg.
The 56-year-old has previously been assistant manager of the German national team and he has been linked with the manager's job.
World Cup winner Joachim Low is set to leave his post at the end of Euro 2020, following 15 years in charge of the team, and Flick is favourite for the role.
RB Leipzig manager Julian Nagelsmann is favourite to take over in Munich from the outgoing manager but former teammate of Flick has criticised Lothar Matthaus for making the suggestion in recent weeks, saying, "A few experts get information from their favorite partners and give it to the public.
"From the outside, speculation is ignited that is so far away that I can only shake my head. That is not appropriate."
Flick became Niko Kovac's assistant at the Allianz Arena in July 2019 and soon became the interim boss when Kovac was sacked that November.
The former Bayern midfielder turned the team's fortunes around and was soon offered the job on a permanent basis.
They went on to win their eighth league title in-a-row last summer and added the Champions League trophy by beating PSG in the final in August.
Featured Image Credit: PA
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