Travel from Prague to Budapest

It depends what do you mean by best. Fastest? Cheapest? Most comfortable?

There is a direct train, running every two hours. It takes a little bit less than 7 hours, which isn't much longer than flying, if you take into account the getting to and from airports, checking in, waiting at the luggage belt etc. And the train is much more comfortable than a plane.

Last time I went from Budapest to Prague, we stopped off a day at Bratislava and 4 days in Vienna. All the trains were not the fast, modern trains like you see in France and Italy. They were old, smelly and rather hot rides--even in April. A men's soccer team got on the train and booted us into another car with some rather intoxicated young men.
That's why I limit myself to 3 1/2 hour train rides. Otherwise, I'm taking budget airlines from place to place or rental cars if in the same country.

David's information is obsolete. Trains are modern, with AC. Although not as fast as in France and Italy, they are going up to 100 miles per hour. It takes little bit less than 7 hours. You can break your journey in Brno or Bratislava. Vienna is not on the direct train line Prague to Budapest. But you can go first to Vienna (about 4 hours) and then to Budapest (less than 3 hours).

Thank you for your suggestions. Has anyone flown? How far in advance of the flight do you need to be at the airport? Ryanair has a one hour flight. Thanks

I would also take a flight--like others mention, a 4 hr train ride is my limit. Whenever I've flown within Europe I arrive at the airport at least 2 hrs in advance.

Czech Airlines, about $125. 2 hours on the Czech side which includes time to get there, check in and eat breakfast at the airport, then 1.5 hour flight followed by about 1 hour to get your bag and get to the heart of the city in Budapest; for a total of 4.5 hours. For me it's a no brainer. You will be checked into your hotel, un packed and cleaned up to have drinks on the Danube Corso by noon.

Much of the train rolling stock is older. Not terrible, but older. No RailJets....

The CD (Czech) trains are very nice, comfortable, electronically equipped. I had planned a night train ride with the CD train from Wien Hbf to Prague on the this last trip but lazied out. Still I took the CD trains to Brno and Slavkov (Austerlitz) r/t this time.