Update (22 August): WARNING: construction works on the railway
Unfortunately, there will be construction works under way both on the main line from Prague to České Budějovice (throughout the whole congress) and the branch line to Český Krumlov (should end on 13 Sep). On both legs, the trains will be replaced by buses on a part of the journey.
To avoid the multiple changes and possible delays, our advice is to consider using the bus service instead.
Really unfortunate timing :-(
Travelling by train is comfortable and could be slightly faster than by coach, but there are fewer connections and in most cases you have to change trains in České Budějovice (Budweis). The regional trains on the branch line to Krumlov are operated by a private company, so you have to buy two separate tickets if changing trains.
You can use this service to search for train connections:
There is one direct train a day in both directions, operated by the state railway company - ČD (České dráhy):
9:04 Praha hl. n.
11:51 Český Krumlov
14:07 Český Krumlov
16:57 Praha hl. n.
Tickets for ČD (České Dráhy) can be bought either at the station or on-line.
Tickets for connecting trains operated by GW Train are sold on the train or on-line
The tickets do not have to be booked in advance.
The trains leave from the Main Station - Hlavní nádraží (hl. n.).
The public transport system in Prague is up to (or above) the European standards. Frequent bus connections link the airport to the Metro (tube/underground) system and tram lines.
Search for connections at https://www.dpp.cz/en
(you can type "hlavni nadrazi" without the special characters in the search interface).
It is recommended to book cabs on-line or at the airport. If not necessary, avoid arranging a ride on the street (some Prague taxi drivers have been known for ripping off tourists). Alternative services, such as Uber, are also available.
The train station is located slightly over 1 km from the city centre and the footpath leading to the town descends down a steep slope - see map.