No trains from Prague to Cesky Krumlov?

Have you checked with ČD? The company that actually runs the trains. www.cd.cz

Rail Europe is not recommended here. It's a third-party reseller that specializes in simple, routine, longer-distance travel, with opaque pricing. It could be said that their target market is novice travelers. CK is a specialized destination, with more local train service. It happens to be hard to get to, and often the fastest route is not by train. Your particular needs will determine the best way to get there.

A national railroad's own ticket website is usually the best source. But sometimes people focus on a particularly good company/country that their trip will pass through, like Deutsche Bahn.

For example, with a large budget and particular needs, we did a one-day runout by car-and-driver from Prague, using Rick's recommended car service. But that's expensive and time consuming, not what everyone wants. Circa 3-hours each way.

Jan,
I like to use Rome2Rio website. I put in your search and found a bus and a train route.

@Tim,
I am looking for a driver for the day from Prague to Telc. Can you share the details of your driver?

We considered a day trip from Prague to Cesky Krumlov but decided it was too far and complicated. Instead we did a day trip to Kutna Hora which was fabulous and easily reached by train. Charming town with interesting history of silver mining, old cathedral and the famous bone church. A UNESCO world heritage site since 1995. Highly recommended and mentioned in RS guidebook.

Well, our trip was in 2007, and I probably got the name from Rick Steves' book. But the service was perfect. I just went through my manila folder from that trip, and I could not find a receipt or the name of the service. I couldn't even find the relevant Rick Steves book in my bookcase. Note that many public libraries have past editions of Rick.

You might want to look further, or find a review-site that you trust. Rick's referrals tend to get so much business that they have to hire more people. Just saying.

https://search.ricksteves.com/?button=&filter=Travel+Forum&query=prague+car+service&utf8=%E2%9C%93

You can click on this search result to filter (Last Two Years), but then it will be much shorter.

Edit: I don't know if my past posts are in that search result, but I have mentioned that while we rarely hire a guide, it paid off that we accepted the car service's promotion of a 90-minute guide. For professional reasons, the historic Baroque Theater at CK (seen only by tour, in English version only ONCE a day). I could not get the ticket lady to understand my English, French or German, but the guide cheerfully bought our tickets for later in the day, for us. It's easy to get Castle tour tickets, however, with many more entry times.

https://idos.idnes.cz/en/vlakyautobusymhdvse/spojeni/
look at this website and put in dates/times of when you want to travel, will give you various options

Thanks guys!

Perhaps the dates you are using are too far in advance and train tickets are not yet available.

I used CK Shuttle from Cesky Krumlov to Vienna, with excellent advance booking service and on-the-day hotel door to hotel door service. They also run shuttles between Prague and CK:
https://www.ckshuttle.cz/transports/transfer-from-prague-airport-to-cesky-krumlov/

Trainline.com shows no trains going all the way from Prague to Cesky Krumlov. There likely is track work being done and part of the route is completed by bus.
My suggestion is to just take the bus from Prague Florenc station all the way to Cesky Krumlov. Not only is it faster, the bus is actually more scenic as you get to see the town squares of a number of the Czech towns on the way to Krumlov.