Airport Transportation for 6 AM Flight

Your hotel can arrange for a taxi. That's what we've done for early flights when public transit either wasn't running or the timing made it just too early. Taxis will be available 24/7, but it's good to arrange it ahead of time to reduce waiting. In other cities we have arranged a shuttle car - book online and it shows up at the appointed time. I have not done this in Prague, but I am sure you can find a company that does it if you prefer that to a regular taxi. I used Welcome Pickups for the exact same scenario in Athens, apparently they have a Prague service as well. I can say that in Athens it was perfect - the driver arrived at 4AM as scheduled, and dropped us off right at the door for our airline check-in.

Uber is another option, I have used it during the day but I am not sure about the amount of cars out at 4AM.

The airport isn't too far from the center and you won't hit much traffic that early. I don't think it's worth it to stay at the airport in order to avoid a 25 minute cab ride. Think of the hassle of moving and the lost time your last night (I'd rather hang out in Prague vs. the airport area!)

fly back to the US (there is a layover so I believe most of the immigration/customer proceedures will take place at the connecting airport and not in Prague)

Depends which connecting airport. If connecting in the Schengen Area, then passport control takes place there. If connecting outside the Schengen Area (for example London), then passport control takes place in Prague.

Flight at 6 am. They want you to be at the airport 2 hours ahead e.g. 4 am. I think 4:30 would be still enough. For flights this early I stay at Marriott - walking distance (about 5 minutes) to both terminals. True, that early the traffic is very thin, but you still have to get up even earlier.

We stayed in the Prague center city, and our B&B arranged for an early morning pickup. We were flying out about 9:00 a.m. I think it took about 20 minutes to get to the airport as it's not that far.
Remember that it's bad enough to have to fly 10 hours or more home--without being up all night getting ready for such an early pickup. But those 6:00 a.m. flights are to other European gateway cities where you're going to be sitting around until a midday flight to the U.S.
Next time, take a 9:00 a.m. flight if at all possible. Most times there are alternative flights that are not so early.

Ditto Mira’s advice. We were in Prague spring 2018 with 6am flight to Frankfurt. Our hotel arranged for a taxi the night before. The only problem we had was the taxi driver would only take cash— we had been told by the hotel desk clerk we could pay with credit card. We had purposely spent all our cash the night before to get rid of Czech crowns.

worth booking an early morning shuttle with this company.
http://www.praguetransport.com/
actually run by an American expat and his Czech wife, that time of day should only take about 30 minutes from the centre of Prague to the airport.

From the center to the airport plan at least 30 minutes, in rush hours one hour.

One thing I learned the hard way - if you do the airport hotel route check how you get from the hotel to the airport! If it’s a shuttle bus, how often does it come? Pick the wrong airport hotel and you save very little time.

A cab from a city hotel can be booked for any time you choose. Say you choose 3:45 to get to the airport at 4:15. Great, you are all set, leave Prague hotel at 3:45.
Now say you are in an airport hotel with a shuttle every half hour on the half hour. So it comes at 4. Congrats, you just saved a whole 15 minutes vs the 3:45 time in the city. I personally would not find moving hotel and spending a valuable trip night in an airport area worth it for a 15 minutes later wake up. Figure out your threshold and the potential time savings!

Mira is right. You won't save much time if you need shuttle to get to the airport. That's why I stay in Marriott - 5 minutes walk to both terminals.

Agree with Mira above. We had a 6:30 am flight from Prague to Brussels (connecting to our transatlantic flight back to the USA). We enjoyed staying in a hotel in the center of Prague and didn't want to relocate to an airport hotel for the last night. It was easy to have our hotel have a cab ready whenever we asked for it. Traffic was nonexistent at 4 am, the taxi ride to the airport was quick, easy, not expensive. Would do it the same way again.

Thank you everyone! I reached out to a recommended transportation service that has confirmed they would be available to pick us up and take us to the airport that early in the morning. The cost for this will probably end up being cheaper than it would be to take public transportation to the airport hotel to check in and leave our bags and then get transportation back to the city to enjoy our last evening and then again to go back for the night. Saves a lot of time and hassle, too. You're right - makes more sense :-) I've book the full 3 nights stay inside the city of Prague.

Thank you!

Smart choice, you'll be glad. Enjoy Prague!

yes, good choice, have a great time . I am back in Prague in just over 2 weeks time.

I took Uber last summer at 3:30 am and it was about $25 and very quick with little traffic. We've also stayed at the Holiday Inn Airport which has free shuttle and Courtyard by Marriott is right across from the terminal. Interestingly enough, there is also a lounge where you can rent rooms/beds for the night at the airport for fairly economical price (cheaper than the hotels at airport). I was going to do it last summer but had a hard time figuring out with having to check your luggage in storage since the rooms are within the secure area and I was too afraid the luggage storage counter wouldn't be open in time to catch my early flight.