Flick was promoted from the coaching staff after Niko Kovac’s dismissal, following Bayern Munich’s 5-1 thrashing away to Eintracht Frankfurt last month.
He was initially hired for two matches, against Olympiakos in the UEFA Champions League and against Borussia Dortmund in the league.
But after two wins he was trusted to continue until the winter break.
Following Bayern Munich’s 2-0 win at home to VfL Wolfsburg on Saturday, CEO Karl-Heinz Rummenigge and sporting director Hasan Salihamidzic agreed that continuing with Flick is “explicitly a viable option”.
“Under him as head coach, the on-field development has been outstanding, both in terms of the quality of our play and the results achieved.
“We set a new record in the 28-year history of the UEFA Champions League with six wins in six matches in the group stage, and in the Bundesliga we have returned to touching distance of the top of the table,” Rummenigge said in a statement.
Bayern Munich currently sit third in the Bundesliga standings, four points behind leaders RB Leipzig ahead of the mid-season break, and have been drawn against Chelsea in the Champions League last 16.
“I am happy that FC Bayern is continuing to place trust in me as head coach.
“Now we are recharging our batteries, and we’ll prepare ourselves intensively for the second half of the season at the training camp.
“Then, we’ll try to achieve as many victories and titles as possible, ”Flick said.