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.
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.