Prague, Vienna and Budapest Travel in Septmber

We are planning to travel to Prague, Vienna, and Budapest for a total
of 15-16 nights ( approx 5 nights in each city). Is that enough time
for each city? First time in each city.

Yes, that’s a pretty nice trip. Research them all and decide around your interests if you want to do more or less time in one city or another. They are really 3 totally different animals.

Most flights are showing a layover from 90 minutes to 2 hours. Air
France has a 2-hour layover at CDG. Is that enough time to catch the
next flight?

This is generally personal comfort levels. 90 minutes is a bit tight for my nerves but it does generally work. 2 hours is much better on my nerves but I like 3 hours. For CDG, I really don’t care for CDG. It and LHR if it were me would be a minimum of 3 hours. But 2 should work.

Also, we are planning to rent an apartment with kitchen in each city.

I prefer hotels, so can’t help. In Budapest if the apartment is in District VI, be careful as most have been illegal since the start of the year. If its not in District VI, then maybe its in a lousy location for a short trip. But as you find them, if you post them here, I will tell you if I know anything about the neighborhood they are in.

September is one of the best times to be in Budapest. But check the events and dates and that might help you decide with your schedule: https://community.ricksteves.com/travel-forum/hungary/updated-budapest-events-for-january-june-2026/replies/new
Some other resources for Budapest that might be helpful
Hotels https://community.ricksteves.com/travel-forum/hungary/budapest-updated-hotel-list
Performance Venues https://community.ricksteves.com/travel-forum/hungary/updated-budapest-performance-venue-list
Restaurants https://community.ricksteves.com/travel-forum/hungary/budapest-restaurant-tales
RS Visitor Meet Up List https://community.ricksteves.com/travel-forum/hungary/hungary-rs-forum-members-meetup-thread

North to South or South to North. It really doesnt matter. I assume you will do the train. If for some reason your flight home is better out of Vienna then there is a way to make Vienna last if you fly between Prague and Budapest. But train is preferable most of the time.

Prague to Vienna, check OBB and Czech Rail and Vienna to Budapest, check OBB and MAV; usually OBB is the most costly option. But not always.

I only want to add to the existing excellent replies. For travel between Prague and Budapest, the Regiojet train is great too. I actually prefer it and have used it on a recent trip to Budapest. Regiojet goes between Prague and Vienna too. Tickets can be bought at regiojet.com. There's also Flixbus between Prague and Vienna but it's only about 10 minutes shorter and it takes you on the D1 highway, which is the busiest one in the Czech Republic and often encounters traffic jams etc.

Veronika is correct. My oversight. And since Regiojet is an independent business without taxpayer funding it has realized it has to provide more for the dollar; and it appears that they do. Only a small minor negative about using Regiojet in or out of Budapest. The OBB and MAV trains go to the spectacular old Keleti Station. Keleti is a worthy experience. The Regiojet trains go to Kelenfold which is a Cold War train "bus stop" outside the center of town. From a stand point of function, they are both served by a metro, trams and buses so from station to the town center is about the same from either.

Thanks everyone for your suggestions. We will be landing in Prague, then in Vienna, and back home from Budapest.