Recognisable Sydney landmarks feature on the double-sided medal, including the Opera House and Harbour Bridge, which are part of the 42.2km (26.2 mile) course.
Users on social media noticed the shape of the stadium engraved on the medal appeared to be carved in the wrong likeness.
Munich’s Allianz Arena is sculpted by thousands of diamond-shaped inflatable cushions, while Sydney’s similarly named Allianz Stadium has a flatter facade smoothed with long bronze fins.
Sydney Marathon confirmed runners would receive the medal depicting the incorrect city’s stadium, noting: “It’s a beautiful medal, and now a little more unique.”
“It’s certainly given everyone something to talk about this weekend, mostly in good humour.”
Germany’s Allianz Arena also poked fun at the mistake, writing on Instagram: “Oh wow, we didn’t have that on our bingo card!”
“Perhaps they tried to find something else they had in common: Allianz Arena — Sydney Opera — Unique Architecture — Both are worth a visit!”
The reverse side of the Sydney Marathon medal shows a gold and indigo pattern designed by First Nations artist Ambrose Killian, widely commended for its ornate pattern.
He confirmed to the BBC that he was not involved in designing the other face of the medal engraved with the wrong stadium.
Some 40,000 runners will take part in the event on 30 August, following more than 120,000 ballot entries.
Organisers praised record participation and fundraising for this year’s event.
