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Munich to Prague

Could anyone suggest the best way to travel from Munich Airport to Prague? We will be traveling in late August. Thank you.

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You could go into Munich, to the bus station (ZOB) at Hackerbrücke S-Bahnhof, and take the IC bus non-stop to Prague. You can do that with a discounted, advance purchase ticket (but you risk the chance of your plane being late). Be sure to specified "Muenchen Flughafen" to "Prague" when looking for the ticket so the S-Bahn will be covered too. I don't know if they still do it, but at one time the last bus of the day also stopped at the airport. Update: Still does. The 5 pm (17:00) bus from Hackerbrücke stops at the airport at 17:45 on the way to Prague.

You can also take the bus to Freising Bahnhof and catch one of the four direct ALX trains going to Prague, with a fully flexible, Bayern-Böhmen-Ticket. It takes about an hour longer, but no risk of losing your ticket if the flight is late.