Striker Robert Lewandowski has enjoyed another superb season for Dortmund, with his haul of 20 Bundesliga goals enough to earn him the division’s top scorer award as Klopp's side again finished a distant second behind Bayern.
However, this weekend's game in Berlin marks Lewandowski's last in a Dortmund shirt, as the Poland international is joining champions Bayern on a free transfer ahead of the 2014-15 season.
And that means Klopp must make the difficult decision over whether or not to start his leading marksman against his future employers.
The 46-year-old opted to leave Lewandowski on the bench for Dortmund's Bundesliga trip to the Allianz Arena last month.
That decision paid dividends as the searing pace and clever movement of his new-look front four - Henrikh Mkhitaryan, Marco Reus, Jonas Hofmann and Pierre-Emerick Aubameyang - inspired a stunning 3-0 win.
However, Klopp is sure to remember Lewandowski's impact on the 2012 Pokal final against the Bavarians, when he scored a hat-trick in a 5-2 rout that sealed Dortmund’s maiden league and cup double.
And the Poland international's public declaration that he is focused entirely on Dortmund's quest for a fourth Pokal crown may also sway Klopp's judgment.
"At the moment, I'm not interested in my new employers at all… I want a crowning glory, preferably with a cup in hand," Lewandowski told Sport Bild this week.
Regardless of whether or not Lewandowski starts, Dortmund will head into the clash high on confidence having lost just one of their last 12 games in all competitions.
Klopp's men also hold the edge in recent Klassiker meetings, as they have won two of their three matches against Bayern this term.
Dortmund ensured Pep Guardiola's first competitive game in charge of Bayern was a miserable experience by running out 4-2 victors in the DFL-Supercup last July, although the Spaniard responded by masterminding a 3-0 Bundesliga success at Signal Iduna Park in November.
Guardiola was tactically out-manoeuvred in the clubs' encounter last month, though, as Mkhitaryan, Reus, Hofmann and Aubameyang tore Bayern's high defensive line to shreds while inflicting the champions' first home league defeat since October 2012.
Bayern's form has been patchy since they wrapped up the defence of their Bundesliga title in March, with their 12 games in all competitions since yielding just six victories.
However, the 16-time Pokal winners will be eager to end their season on a high by completing a second straight domestic double.
Guardiola will definitely be without Thiago Alcantara for Saturday's tie after the midfielder tore knee ligaments in training on Monday, while Bastian Schweinsteiger is a doubt with a knee problem of his own.
Marco Reus limped out of last week's 4-0 season-ending win over Hertha Berlin, but the attacker will be fit for their return to the Olympiastadion - meaning the Lewandowski predicament represents Klopp's only selection headache.
