Munich to Prague: Transportation?

Take the train, here is the site we use to book directly:
https://int.bahn.de/en
Flixbus is a good option; they list the travel time as less than train at about 5 hours 30 minutes; the bus usually makes a rest stop.

We booked directly with the Czech (CD) train system to travel between Prague and Munich and back: https://www.cd.cz/en/

We found that is less expensive than using the DB site, and seat reservations were free. We traveled the CD system quite a bit while based in Prague and never had a problem.

The sites you listed for train tickets are 3rd party resellers, which may explain the bad reviews.
Using the sites the others have listed is the way to go.

Flixbus is reliable in general and appears to take an hour or so less to make the trip. It also
is direct and you don't have to make multiple connections as you would on the train. The bus
is comfortable, but you can't move around quite as easily.

No matter how much you (over)analyze the possibilities, there is always some chance that
your hopes for best execution will fall short on any one individual journey.

In this situation, I'd take the bus. It's a bit faster, same price or cheaper, and derisks the
potential of missing a connection.

I did this route three weeks ago. But I did it differently.....

Lufthansa.

Normally the direct train takes 5 1/2 hour, and I would prefer it over the bus. But in July the direct train is not operating because of engineering works.

On your date, I'd take the bus. Because of the construction site mentioned above, you would have to take a replacement bus between Regensburg and Schwandorf. This will be overcrowded and the journey time will be longer. The Flixbus may be half an hour late because of traffic jams on the highway, but it will still be faster. It's air-conditioned and there is enough space in the trunk for your luggage. The Flixbus departs from Munich ZOB, directly at the S-Bahn stop Hackerbrücke (1 stop with any westbound S-Bahn from the main station).

PS. I would never book a ticket with RailNinja; the reports of inflated prices and non-delivered tickets are legion; as a rule, it is best to book with the carrier itself.

Don't spend 6-7 hours on a bus! Fly! It is less than a hour flight. Why waste a whole day traveling from Munich to Prague. You can leave at 8:30am and be in Prague by 9:30am and enjoy the whole day in Prague instead of sitting on a bus or train for 6-7 hours. $160 a ticket. Well worth the time and comfort.

Thank you, everyone for your responses. The variety of the options spoken to and the detail are just what I needed for confirmation and orientation!

I’ve driven Prague to Regensburg and thought it was a beautiful drive, so a mark against flying.

Don't spend 6-7 hours on a bus! Fly! It is less than a hour flight. Why waste a whole day traveling from Munich to Prague. You can leave at 8:30am and be in Prague by 9:30am

However, this comparison seems a little truncated. First of all: the journey with the Flixbus takes 4:50, not “6-7 hours”. Secondly, you have to add to the one hour flight time: 1 hour from the center of Munich to the check-in point, at least 1 hour time cushion for possible traffic delays, orientation, check-in and security, 45 minutes from deplanning to public transport, 30-45 minutes to the center of Prague, making a total of 4:15 - 4:30: with the flight you gain roughly half an hour for twice as much hassle and four times the price.

Even if it were the same time period, I would rather fly than sit on a bus for nearly 5 hours.

At the airport, I can stretch my legs, get a coffee or a bite to eat, find a quiet corner until my flight.

If I don't like the people sitting around me, I can move at an airport. On a full bus, you may be stuck next to "who knows who."

If money is the issue, then a bus or train is much less expensive. But, if time and duration of travel is more important, then flying wins hands down.

Why sit on a bus for even 5 hours when a flight is 55 minutes? I prefer to be at my destination as soon as possible. Time is the most valuable commodity when travelling and being stuck on a bus instead of being in the old town of Prague isn't my preferred choice. However, the OP's husband and daughter can make the call as to how they want to spend their 5 hours.

Interesting to note how some people buy into “getting there is half the fun,” while others think getting there is no fun at all.

Interesting to note how some people buy into “getting there is half the fun,” while others think getting there is no fun at all.

And sometimes it could be either or....it depends on the route.

Conclusion: we booked FlixBus travel from Munich to Prague. Every response to my question was helpful in this choice. For future readers with this same question I'll waterfall why:
1. Before posting the original question I considered flying. I know what to expect w flying. However, tickets were at least $200/ticket one way and my math says that even a 1 hour flight is 4-5 hours w boarding, exiting, taxi on the runway, etc. So $600 and maybe an hour fewer than the bus.
2. Train: fastest was 5:40 in duration and I do like that we could move around within the line of connected tubes. $45/ticket. However, with the train came at least 2 changes of trains and exhortations that "the time to change between trains was short -- 7 mins, 15 mins -- and to be certain we could make it! This risk was 100% transferred to us with no direction that passengers typically succeed. I'm not experienced in the stations, how far apart the train platforms are, or if the incoming train allows a reasonable period of time to grab our luggage and find the next train. And we'd have to do it twice. Lastly, the note about the train track section being under repair and needing to jump on to a bus to get around it -- well, that's a 3rd change of train without disclosure. The train would be purchased stress, the worst of the 3 options.
3. FlixBus: $29/ticket. 5 hours, direct The bus offered the comparatively premium experience of storing your luggage and arriving. For the price we were able to choose our seats and opted for the panoramic seats in the front row of the 2nd story of the bus. We could also have chosen seats with a table between 2 rows of seats (like you find on trains), or the most economical option, regular seats like you'd find on a train or plane. Wifi and plugs on-board. I also liked that I was able to book direct w FlixBus. The booking sites disintermediate the experience and accountability for it. Booking sites take no responsibility that what was purchased was delivered, mark up the cost considerably, and offer service through bots only or delayed humans. Rail Ninja especially. So, so, bad.

This was the first time I've posted in this forum. Your responses exceeded my expectations. I'm grateful for your help in ending my 3 months of spinning . . . .thank you, thank you!!