Berlin to Praha / Prague / Prag by train

DB is the national railway operator in Germany, so its website can be used for booking journeys by German express trains; the ICE and IC trains and it doesn't charge booking fees.
It also sells tickets for journeys by direct trains on all international routes from Germany regardless of whether DB is operating the train service.

It also sells an extensive range of end-to-end journeys which involve making connections both within Germany and in neighboring countries, but journeys between Germany and Britain cannot be booked on DB.

A key feature of DB website worth keeping mind is that it offers 1st class ticket purchasers complimentary seat reservations on journeys both within and to/from Germany.

Seat reservations for daytime in both 1st and 2nd class can also be booked separately from tickets.

CD is the national rail operator in Czechia and its very smart online booking service sells tickets for all express train services which it operates within Czechia, as well international journeys by EC, Railjet, SuperCity and overnight trains.
Some express trains, both within and to/from Czechia are operated by LeoExpress and Regiojet and these cannot be booked with CD.

CD also sells international tickets involving changes of train outside of Czechia for end-to-end journeys:

• to Belgium
• destinations in Germany not served by direct trains
• to Paris
• to Arhus, Copenhagen and Odense in Denmark
• to destinations in Italy served by the overnight trains from Austria
• to Luxembourg
• to destinations in the The Netherlands, including Amsterdam, which are on the route of the direct trains from Berlin
• to destinations in Romania, including Bucuresti served by the direct day and night trains from Budapest.

In addition to tickets, seat reservations, reservations for bicycles, plus reservations for couchettes and sleeping cabins, can also be booked online with CD, with no booking fees.

Omio is an online ticket agency which offers tickets for rail journeys in France, Germany, Great Britain, Italy and Spain.

The three key advantages of using Omio are

• it offers prices in multiple currencies
• it usually offers price comparison with other modes of travel including flights and buses
• when visiting Europe, you can book journeys in multiple countries in one transaction.

The disadvantage of booking with Omio is that it often adds a booking fee to the final price; therefore when it does so without offering a price advantage, SMTJ doesn't tend to offer Omio as a booking option.

Happy Rail is a Netherlands rail ticket agency which sells tickets for both national and international journeys within a range of countries including Belgium France, Germany, Sweden, Switzerland.

HappyRail doesn't charge booking fees in the conventional sense, but if you're not Dutch you can expect to pay additional transaction fees, which will be added to the total cost.
That's because the most common form of online payment used in The Netherlands is 'iDEAL' and HappyRail doesn't charge a transaction fee for 'iDEAL' payments, but only Dutch residents can sign up to 'iDEAL'.
Other forms of payment include Visa debit cards will incur a fee.