With the Gunners in need of a confidence boost after seeing their hopes of a first Premier League title since 2004 all but extinguished by the recent loss to leaders Chelsea, the Frenchman will no doubt be desperate to mark his European milestone with a positive result.
The bad news, though, is that Wenger will be pitting his wits against a coach with a far better Champions League record than his own, Carlo Ancelotti.
After getting his first taste of the competition with Monaco, whom he led to the semi-finals, in 1993-94, Wenger moved to Arsenal, where he has pulled off the feat of securing qualification for a remarkable 18 consecutive seasons.
He has yet to get his hands on the trophy, though. Arsenal did reach the final in 2006 but the 10-man Londoners suffered the agony of seeing Barcelona come from a goal down to triumph 2-1 in Paris.
Furthermore, Arsenal have now been eliminated at the round of 16 for the past six seasons, which doesn't bode well going into this week's meeting with Ancelotti's Bayern.
The Bavarians have yet to truly impress since the Italian's arrival at the Allianz Arena last summer but the former midfielder's European Cup credentials are mightily impressive.
Indeed, Ancelotti is one of only seven men to have lifted the trophy both as a player and a coach (Miguel Munoz, Pep Guardiola, Giovanni Trapattoni, Johan Cruyff, Frank Rijkaard and Zinedine Zidane are the others), and only the second manager after Liverpool legend Bob Paisley to have won it three times.
Ancelotti triumphed twice during his time in charge of AC Milan, edging out Juventus on penalties at Old Trafford in 2003 before gaining revenge over Liverpool for 'The Miracle of Istanbul' in 2005 by defeating the Reds in Istanbul two years later thanks to two Pippo Inzaghi goals.
His third triumph came three years ago, when he led Real Madrid to 'la Decima', their long-awaited 10th European Cup success.
Ancelotti is now hoping to become the first coach to win a fourth title - and the first to triumph with three different clubs.
Certainly, his chances of getting past Wenger look promising. Ancelotti has won 56.49 per cent of his 154 Champions League games, while Wenger's win percentage is 49.25.
However, it is their respective records in the knockout stages that really sets them apart, with Ancelotti having won nearly half of his knockout games (46.3%), while Wenger has lost nearly as many of his (41.9%).
That fine win rate is why Ancelotti has managed to triumph in a staggering 21 of his 29 knockout ties (including finals), compared to Wenger's return of eight successes from 23 ties.
The former Italy international has made 10 previous appearances in the last 16 during his time in charge of AC Milan, Chelsea, Real Madrid and PSG - and won an incredible eight of those ties.
By contrast, Wenger's success rate is just 35.8%, having claimed victory in just five of Arsenal's 14 last-16 encounters.
Wenger has also won just two of his six quarter-final outings, whereas Ancelotti boasts a 66.67% success rate in both the last eight (6/9) and the semis (4/6).
In addition, Ancelotti only tasted defeat in one of his four finals - and even that was a game that he should have won, with Milan having famously blown a 3-0 lead in their epic clash with Liverpool in Istanbul in 2005.
All things considered, Wenger has it all to do to ensure that his 200th Champions League outing is a successful one.
Still, the Gunners boss may take some encouragement from the fact that on the one previous occasion he faced an Ancelotti side in the last eight, he came out on top, with Arsenal defeating Milan 2-0 on aggregate in 2007-08 thanks to late goals from Cesc Fabregas and Emmanuel Adebayor in the second leg at San Siro.