Use Eurail German Rail Pass to Prague

Basically pick your train from Berlin to Prague, then go to the train operator (German or Czech) and buy a ticket on that site for the matching train number, using Schona as the departure, and Prague as the destination.

The problem may be that on DB, the German site, you may not be able to purchase just the Czech potion, or more likely, the train may not actually stop in Schora, so not giving a solution for that route. You may be able to go to a DB office at a station though and purchase a supplement for your journey. The other alternative may be to take a train to Schora, then transfer to another train from there.

Thread warning: Many will probably question whether the German Eurail pass was really the best option given other options and your itinerary, but if you already have the pass, that is water under the bridge.

It may be to your advantage to re-arrange your itinerary. Do you have any plans to be in Munich or in Regensburg, Germany's best-preserved medieval city? Specal fares to Prague (Prag-Spezial) are available for DIRECT trains to Prague which cost just €36.50 from Regensburg and €55 from Regensburg. You don't have to pre-book these tickets. Just buy them on the day of travel and hop on. You can use the ticket for any of the regional train journeys that same day; hop off for sightseeing in any town along the way you like, then hop back on to finish your trip with a subsequent regional train. This option - and other options - are mentioned at the web's best overall resource for train information:

https://www.seat61.com/trains-and-routes/munich-to-prague-by-train.htm

There may be some helpful advice here for the route from Berlin as well:

https://www.seat61.com/trains-and-routes/berlin-to-prague-by-train.htm

Note that OMIO is mentioned on the above pages as a possible vendor for tickets to Prague from Germany

I would buy a standard-fare ticket from Bad Schandau (just before the Czech border) for CZK 565 (approx. €23) on the Czech Railways website (CD.cz). Schöna is not a fare point for CD, but at the DB website a ticket from Schöna to Prague is €36 (meaning they charge €13 for the 3 km to the border: caveat emptor).

Easiest is to probably just go to the station, and ask for a ticket form the border to Prague. You can split tickets at the border, even though the train does not stop there. I used to do that a lot in the past for trips to Belgium when I still had a Bahncard.

Easiest is to probably just go to the station, and ask for a ticket form the border to Prague

Unfortunately not. One of the many minor annoyances that DB has come up with in recent years is the removal of border tariff points from ticket sales. This means that you cannot buy a ticket to/from the border, but only to/from the last station before the border.

The two cheapest options for rail pass holders on the German side are therefore (1) as described above, the international ticket from Bad Schandau to Prague, purchased from CD.cz (565 czk). (2) Ticket from the first station in Czechia, Dolni Zleb (265 CZK). For the gap between Schöna Grenze and Dolni Zleb, you can buy a ticket (and possibly a small supplement for the long distance train) from the Czech conductor, which is very straightforward and dirt cheap. I do this from time to time for the border crossing Furth im Wald/Czeska Lipa or Schirnding/Cheb.

BTW, if you enter "Schona" on the Bahn website, you might have trouble finding it. The spelling is Schöna. If you can't make an ö, you can use oe, but simply o won't work.

The express train from Berlin to Prague used to be (2012) an EC. It looks like today it's a RailJet. That train stops in Bad Schandau, then, next, in Decin. It doesn't stop in Schöna.

I think the easiest thing here is to buy the tickets from Czech Rail from Bad Schandau to Prague. If, for some reason, you can't do the CD.CZ thing, then the next best thing might be to go to Schöna (3,20€ from Bad Schandau) and buy your Czech Rail ticket to Prague, there. There is an S-Bahn out of Dresden that goes to Schöna via Bad Schandau. You could probably get off at Bad Schandau and take the S-Bahn to Schöna. At the worst, you could just bite the bullet and buy tickets from Bad Schandau to Prague from the Bahn at about 45€/person, full fare, possibly cheaper for an advance purchase Sparpreis ticket. Currently, Sparpreis for Monday is 27€, Super Sparpreis is 24€.

For Friday, 27 Feb (in about 2 weeks), I see Super Sparpreis fares of 18€ from the Bahn.

Someone above may have said this, but do check the Czech Rail cost on the Prague ticket. It might surprise you.

Thank you all.
A lot of information to digest.