We will be traveling from Budapest to Vienna, staying for 3 nights, then to Salzburg for 2 nights, then on to Munich. Is it possible to buy a train ticket for budapest to Munich that allows for stopovers, or is it better to buy the tickets point to point? The website bahn.de doesn't allow for inputting stopovers that I can see, so not sure if that is allowed. Does anyone know the answer?
train tickets from Budapest to Munich?
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In terms of stopovers, generally if you have an open ticket (the kind that permits travel in a certain time period) then you can get on and off the train but that will usually only apply to local regional trains when there are multiple services throughout the day.

It can really differ from country to country and train to train. The fastest train connections between Budapest and Vienna and Vienna and Salzburg are by high speed Railjet so I would advise buying point to point tickets in advance. Looking at prices for 3 months time you're looking at £35 ish for the Budapest to Vienna and £45 for Vienna to Salzburg. If you went all the way from Budapest to Salzburg it would be around £75 so not much less than these 2 individual tickets combined really.
From Salzburg to Munich there are tons of departures by Railjet InterCity and Eurocity which I'm sure you've seen over on DB. The cheapest tickets are €19 and take less than 2 hrs. Hope that helps!
Happy railing