The shock revelation came after Saturday’s 3-2 win at Wolfsburg left the Bavarians seven points clear at the top of the Bundesliga.
The 56-year-old, who steered Bayern to last season’s treble which included the Champions League title, told the squad before making the news public.
“I told the team that I informed the club during the week that I want out of my contract at the end of the season,” Flick said.
“It was not an easy decision for me.
“It was important that the team heard it from me.
“I want to give my thanks and compliments to the club for giving me the opportunity to coach such a team.”
He insists his future plans are unclear.
However, with Joachim Loew stepping down as coach of Germany after the Euro 2020 finals this summer, Flick is the obvious choice to replace him.
Flick was Loew’s assistant coach when Germany won the 2014 World Cup title in Brazil.
The chance to succeed Loew and take charge of the national team is an “option that anyone would have to consider”, Flick later told broadcaster ARD.
However, he insisted his decision to quit Bayern was “independent of the German FA. I’ve simply decided that for myself.”
The news caps a turbulent week for Bayern who were knocked out of the Champions League quarter-finals on Tuesday by Paris Saint-Germain.
Tensions have been simmering behind the scenes between Flick and Bayern sports director Hasan Salihamidzic over player recruitment.
“I have discussed things internally with those responsible. The reasons will remain internal for now,” added Flick, who said he made his decision after “careful consideration”.
The rift was triggered after Salihamidzic confirmed Jerome Boateng will not be kept on next season. Flick made it clear he wanted to keep the 32-year-old centre-back.
Bayern forward Thomas Mueller said Flick did not tell the squad why he wants out.
“He didn’t give us reasons, but he used up a lot of energy in the last year and a half, which has been extremely intense,” said Mueller.
“To be a coach at FC Bayern – you basically need a thick skin.
“A lot is asked of you. It was an intense time.
“He didn’t explain why exactly, but he doesn’t have to justify it to us either.”
Bayern captain Manuel Neuer admitted the squad was still “processing” the news.
“It had an emotional impact on all of us.”
Being released from his Bayern contract would clear the way for Flick to take charge of Germany after the European Championship.
While Liverpool manager Jurgen Klopp and RB Leipzig coach Julian Nagelsmann both firmly ruled out replacing Loew, Flick has always stopped short of following suit.
Flick admits taking charge of Germany is “an option” but claims he has yet to speak to national team director Oliver Bierhoff who will ultimately decide.
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