Arsenal have been knocked out at this point in the Champions League for the last six years running - and will face the Germans for the third time in five years.
They lost to Bayern in 2014 and 2013 - despite winning the second leg 2-0 - but probably face their best chance of progression with the German champions out of sorts.
Arsenal also lost to Bayern at this stage in 2005 but will have something of an advantage this time around because they play the second leg at home.
Bayern came second in their group to Atletico Madrid and lost two of their six games.
They have also only just gone back to the top of the Bundesliga and sit level on points with newly-promoted RB Leipzig.
They’ve drawn three times and lost once in the league as Carlo Ancelotti appears to be struggling having replace Pep Guardiola in the summer.
Arsenal's general secretary David Miles told BT Sport 2: "We thought it might happen, we've played them five or six times in the last 15 years.
"We've now qualified for the knockout stage for the 14th successive season, that's testament to Arsene and the squad over that period.
"The fans will think we've got the rough end of the draw again but at some stage the tide's got to turn so why not this time?"
"Hopefully we can get some of our injured players back and the home game in the second leg will be vital for us. "We're going to be upbeat and positive."
Arsene Wenger insisted anyone can win it this year and with Alexis Sanchez and Mesut Ozil in such fine form will be confident of an upset this time around.
The first leg will be played in Munich on February 15 and the return at the Emirates two weeks later on March 7.
"It looks like no team at the moment is the super, super favourite and everybody can have a chance," said Wenger earlier.
"The quality of the draw - or the luck of the draw - could have a part as well
"We know now after we finished top of the group that our second game is at home so that gives you a psychological advantage.
"We just have to look at it and deal with it after."
Elsewhere Manchester City drew Monaco and Leicester City face Sevilla.
PSG face Barcelona in the other red hot affair while Napoli face holders Real Madrid.
The other ties include Benfica v Borussia Dortmund, Porto v Juventus, and Bayer Leverkusen v Atletico Madrid.
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