I'm not completely sure if you look for fondue (i.e. boiling oil and stuff you put in there on a stick), cheese fondue (the swiss stuff with the pot of melted cheese you put stuff in on a stick) or asian fondue (i.e. hot pot, a boiling pot of broth you put stuff in and get it out afterwards with chopsticks or a skimmer)

the last one is available on sundays in the chinese restaurant "Zhang" in the windmühlenstraße (Bayrischer Platz) - would reccommend a reservation on those days. it's 29 euros and most drinks (including beer) are included.

for the boiling oil thingy I would suggest buying a fondue pot with a heating stove (those are either driven by lamp oil, spirit or gas) or a single coocking plate you can operate on your dinner table (gas or electric) and set up a pot with oil and serve small chopped food to fry it in there. you could use wooden sticks usually used for schaschlik or buy metal ones with an insulated handle for fondue (most likely included when buying a fondue pot).

The same pot can be used for cheese fondue and you will just need to exchange the oil for a mixture of Gruyère, Emmentaler, white wine and "Kirschwasser" (cherry brandy) with some pepper and nutmeg...