Will be taking the train from Frankfurt to Prague with a transfer in Regensburg. It's my understanding that I'm allowed to take a later train from there rather than the next one out as long as my trip ends before midnight. Is this correct?
It completely depends on the type of ticket you hold. Or are you asking about a rail pass?
A trip on one day from Frankfurt to Prague, with a stopover in Regensburg, would require at least 8 hours of train travel. That doesn't leave much time for Regensburg and could mean a very late arrival even with a very short visit in R'burg. Do you already have a ticket? If you are scheduled on an ALX or other regional train for the final travel leg, then yes, you should be able to use a later regional train. When the final destination lies in another country, it is normally possible to take not just a later train the same day, but a later train the next day, or the next day as well. I have bought a number of saver fare tickets with long, multi-day stopovers myself. So if you wished, you could probably overnight in Regensburg - play around with the stopover feature at the DB search page to see if it works, if that's your wish.
Thanks for the replies. In having more time to look into it, there isn't a later train to catch!
I assume you want to use a SparPreis (Savings Fare) ticket for this journey, because a Standard (full fare) ticket for a journey of over 100 km (which this journey is) is valid for travel until the end of the second day. You could easily stop overnight in Regensburg with a full fare ticket.
BTW, SparPreis tickets are train specific only for the long distance train (ICE/IC/EC) segments. For the regional segments, you must finish your travel by 10:00 the following day (not midnight).
The standard connection from Frankfurt Hbf to Prague is an ICE to Nürnberg, an RE to Regensburg, and one of the ALX train to Prague. These connection leave Frankfurt every two hours starting at 6:21. The last connection of the day leaves Frankfurt at 14:21, arrives in Regensburg at 17:24, leaves Regensburg at 18:14 (50 min stopover), and arrives in Prague at 22:16. If you left at 10:21, you could have almost 5 hours in Regensburg.
But it sounds like you won't be able to leave Frankfurt at 10:21, so I am assuming that you are arriving by plane at FRA that day. In that case, a SparPreis ticket is dangerous because it is for a specific ICE to Nürnberg, and if your flight arrives late the ticket is worthless.
Instead, if you are arriving from the US, I would suggest you ticket Frankfurt to Regensburg using a Rail & Fly ticket. These tickets are issued by most airlines for the rail part of your journey from any airport in Germany to any rail station in Germany. They are open tickets, valid for the day of arrival and the following day, and cost 34€ per person and direction. For the following day, a Prag-Spezial-Ticket, for 25€ would take you to Prague. That is certainly cheaper than full fare and avoids the risk of late arrival.
@Lee: I'll be in Frankfurt for a few days before heading to Prague. As my trip isn't until September I still have time. However I can't spend overnight anywhere along the way, just a few hours.
Even at the webshop of Czech Rail, which usually has the best prices, that trip would cost over €100 when bought as a single ticket. So the most economical solution would be to buy a saver fare ticket (Sparpreis or Supersparpreis) for the Frankfurt - Regensburg leg at the DB website (www.bahn.com) and another ticket for the Regensburg - Prague leg at the webshop of Czech Rail (using any ALX train, in Czechia classified as "Ex"; no restrictions). Three months out from today the price for the first leg is 25.90 or 29.90, for the second one 317 czech korunas = €12.50. There are some direct ICE's from Frankfurt to Regensburg (headed to Vienna), no need to transfer to a slow RE in Nürnberg.
Don't book the entire trip at either of the two web sites since they cannot give you a saver fare for the other country.
There are some busses from Regensburg to Prague as well, look up time tables and fares here.