train from munich to prague

Fastest way is via non-shop bus as Larry recommended.

There is only one site, the German Rail (Bahn) website. There are only regional trains directly from Prague to Munich, via Pilsen, Fürth im Wald, and Schwandorf. The best way I know of to get tickets is to buy Prague to Fürth im Wald at the station in Prague for about €10/person (in Kc), then use a €29 Bayern-Ticket, which you can get ahead of time online from the Bahn website for Fürth to Munich. The Bayern-Ticket is an all day pass good for regional trains all day (after 9 AM workdays) anywhere in Bavaria. €29 covers 2 to 5 people, so with 2 people it would be about €25/person. There are also intercity coaches run by the Bahn from Praha hl.n. to Munich Hbf. The bus takes about an hour less than the train. If you purchase online in advance from the Bahn, you can get Europa-Spezial ticket starting at €29/person, but the least expensive fares sell out and the remaining tickets, although still discounted, are more. I see some €29 fares still available for July 2.

The bus is faster, by about an hour. However, to get the €29 fare, you have to purchase online, at least 3 days in advance (I think you can buy it at the counter three days in advance, but there is a fee for personal service). If you buy it just before travel, it's €61/person. On the other hand, you can purchase the tickets for the regional train right up to the time of travel, always for ~€25/person. The four direct trains from Nürnberg or Munich are run by ALX and are nice, modern looking coaches. I was supposed to take one of them from Pilsen to Prague a few weeks ago, but my train from Klatovy was late and the ALX train was pulling out of the station when I arrived. I had to take a Czech Rail train an hour later, and it was nowhere near as nice as a similar ALX train I took a few days later. So when scheduling your trip, try to take the ALX train that goes through/connects in Schwandorf.