Even though they aren’t in neighboring countries, Amsterdam and Prague are both popular with many of the same groups of travelers, so they are commonly strung together on a trip of Europe. Assuming you aren’t planning on hitchhiking (don’t), then you’ve got basically 3 main options to consider, and fortunately all of them are worth considering and not terribly expensive.
The train is the most popular, and if you reserve in advance you might be able to get an affordable bunk in a sleeper car. Buses take the same amount of time and are usually much cheaper, but definitely less comfortable. Thanks to one budget airline, a nonstop flight might be the best option of all if you book early enough to get their best fare.
Trains between Amsterdam and Prague
As of now, there is only one train that directly connects Amsterdam and Prague, but if you are determined you could also patch together your own journey that changed in Berlin or thereabouts, and it might even be a bit faster, though also more expensive. The one official train is an overnight journey that has sleeper cars and some regular cars, and a bunk in a sleeper car can actually be fairly cheap if you reserve and buy in advance.
Promo fare: one-way: €69 in 6-bunk couchette, €79 in 4-bunk couchette
Full fare: €119 2nd class seat and €135 in a 6-bunk couchette (if you buy at the last minute)
The train leaves Amsterdam around 7pm each evening and arrives in Prague a bit after 9am the following morning, so the journey takes 14 hours and 17 minutes. A “couchette” in case you aren’t familiar with this name, is a simple bunk bed, so the 6-bunk couchette has 3 beds on each side of each small compartment. You can pay just a bit more for a 4-bunk couchette if you happen to be going with 3 friends. The bed isn’t any more comfortable, though you do get a bit more room to sit up with only 2 beds on each side.
You can reserve these bunks on the Dutch International train site, and if you reserve early enough you can probably get these special promo fares. If those are sold out you’ll be paying about double if you still want to take the train.
Flights between Amsterdam and Prague
Since both the train and the bus each take about 14 hours, this is definitely a city pair where a cheap flight can save you a lot of time. So many cities are within 5 or 6 hours of Amsterdam by train, and those flights don’t really save you any time due to all the airport transportation and early check-in stuff, but this one is different so check for those flights early on.
The Slovakian discount airline called SkyEurope Airlines has one of its hubs in Prague, and they fly nonstop between there and Amsterdam twice per day in each direction. The flights leaving Amsterdam go around 9am and 9pm each day, and the flight takes about 90 minutes. If you check early enough to get one of their special fares, you can fly between the two cities for around €70 each way.
KLM also flies nonstop between the two cities, but they rarely have promotional fares, and even when they do they will likely be quite a bit more expensive than SkyEurope. Just enter your ideal date into that booking box on the top of this page and hope that SkyEurope has a promotion going. If not, the train or bus is probably a better option.
Czech Airlines also flies this route nonstop, and usually at very high prices. They have a new budget affiliate called Click4Sky, which sells empty Czech Airline seats at a discount, but actually finding these empty seats can be challenging or impossible.
Buses between Amsterdam and Prague
Similar to the overnight sleeper trains that connect these cities, the bus is a decent option because it also saves you a night in a hostel or hotel. For the hardcore backpacker set, the bus is usually a much better deal.
Promo fare: €15 one way, with no additional discounts for students or seniors
These buses are currently running 4 days per week, leaving at 10:30pm on Sunday, Monday, Wednesday, and Friday nights, and arriving 30 minutes after noon the following day. Even if you can’t get the cheap €15 one-way promotional fare, you can probably get a slightly higher fare that will still be less than half of what the train costs.
These Eurolines buses are fairly comfortable, and well set up for these overnight journeys. There will be a couple stops along the way at a rest area or truck stop, and there you can stretch your legs and buy some food.
In order to get the cheapest ticket, it’s best to buy them online from the Eurolines website, which can be quite confusing the first time you use it. You can also buy these tickets from the Eurolines office on Damrak near Centraal Station, although that’s not where the buses depart from. From Amsterdam the bus leaves from in front of Amstel Station in Amsterdam, which is about 2 km south of Centraal Station, and easy to reach by tram or metro.