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Currently, the fastest way to get to and from Prague is by a non-stop, express bus from Nürnberg. These buses are, apparently, run by the Bahn. They take 3¾ hrs to/from Nürnberg and 5+ hrs to/from Munich via ICE to Nürnberg. You can get a Europa-Spezial fare of €19,- per person from Nürnberg or €29,- from Munich. The buses have onboard snack bars and WCs. They can be booked online from the Bahn website; a seat reservation is included with the fare.

Usually a little less expensive, albeit an hour slower, is one of the 3 daily, direct or one change trains from Munich, Regensburg, or Nürnberg. These trains take six hours to/from Munich or about five hours to/from Nürnberg. The table below shows the schedule for these trains.

Munich to Prague >
StationTimes
Dep Munich 4:55 9:0112:44 17:02
Dep Regensburg 6:281 10:31 14:21 18:35
Dep Nürnberg 6:00 9:53 14:0517:36
Ar. Schwandorf 6:54 7:0310:5710:5814:4615:0718:4619:01
Dep Schwandorf 7:04 11:08 15:08 19:09
Ar. Plzen (Pilsen) 8:57 12:57 16:5720:59
Dep Plzen (Pilsen) 9:10 13:10 17:10 21:10
Ar. Prague 10:58 14:58 18:58 22:58
1 Change of trains in Regensburg, 6:20-2:28

Prague to Munich
StationTimes
Dep Praque5:04 9:04 13:04 17:04
Ar. Plzen (Pilsen)6:50 10:50 14:50 18:50
Dep Plzen (Pilsen)7:00 11:00 15:00 19:00
Ar. Schwandorf8:53 12:56 16:53 20:56
Dep Schwandorf8:549:08 13:0313:0916:5416:5821:0521:05
Ar. Nürnberg9:56 14:2317:56 22:23
Ar. Regensburg 9:3713:31 17:2921:33
Ar. Munich 11:1515:02 19:1523:06

For trains from Germany to Prague: In general you can use a €28 Bayern-Ticket to the German-Czech border. On weekend days it is valid all day long. On workdays, it is only valid after 9 AM, so the Bayern-Ticket cannot be used at all on the 4:55 train out of Regensburg or the 6:00 train out of Nürnberg. For the last three trains, Bayern-Tickets will be valid for the entire way on weekdays.

For the part in the Czech republic, German Rail in Munich will sell you an Anschluß ticket from the German border to Praha for appoximately €20. I am told that you can also buy the Czech ticket on the train for about €10 (238 Kc), but I have no confirmation of this.

There is also a Bayern-Böhmen ticket (€33 for up to 5 people) for anywhere in Bavaria to within a transition area in the Czech Republic. Pilsen (Plzen) is in this area. If you purchase a Bayern-öhmen ticket you can ride all the way to Pilsen. Once over the border in the Czech Republic, you should be able to purchase a ticket the rest of the way to Prague for about €5,70.

For trains from Prague to Germany: You can purchase a ticket from Prague to Furth im Wald for about €10 (288 Kc). From the border to Munich, Regensburg, or Nürnberg you will need a Bayern-Ticket for €28.

You probably cannot purchase the Bayern-Ticket in Prague. If you are going to be in Germany earlier, get it then. If not, use the Online Ticket Store on the Bahn website. For two people, the fare using the Bayern- & Anschluß-Tickets would be €23,50; the Czech Rail fare from Prague to Munich might be less. (The fare for the 2/3 of the way in the Czech Rep. is only €10, from them, the rest of the trip might not be much more than €13,50.)

German Rail also has prices for round trips in 2nd class from Munich, Regensburg, and Nürnberg to Prague called a Prag-Spezial. The prices are shown below. Except from Munich, these prices are better for a round trips than the Bayern- & Anschluß-Ticket combinations. The Praq-Spezial ticket would also allow you to leave before 9 AM without buying the point-point ticket.

To/FromFare, RT
Munich€63,00
Regensburg€42,00
Nürnberg€52,00