An S-Bahn driver reported spotting the reptile on Monday evening on the tracks between Schwabhausen and Bachern at about 7:30 pm.
Federal police officers rushed to the scene in a patrol car and found the tortoise strolling blithely along the track near a crossing with the road.
They picked up the 20-kilo beast and found that it was unharmed despite its dangerous choice of escape route.
Workers from the Munich Reptile Society then took the puzzled chelonian into their expert care.
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The police weren't able to identify the species of the tortoise or who it belonged to, but have asked the owner to get in touch.