We are planning a trip of Prague and Slovenia. Our plan is as follows:

Day 1-3 Prague (reaching at 8am on day 1. So, we have full 3 days in Prague)
Day 4-6 Budapest (travel by train from Prague to Budapest- takes 9 hours)
Day 7-8 Ljubljana (travel by train from Budapest to Ljubljana via Vienna- 9 hours)
Day 9-11 Bled
Day 12-13 Vienna

We need suggestions with the following:
1. Should we skip Budapest as we will be using Day 4 (from Prague to Budapest) and day 7 (from Budapest to Ljubljana) in train?

2. In case you recommend that we do Budapest, what is the most efficient way of travel? We don’t have Croatian visa and hence we can’t take a train going via Croatia.

3. If we decide to skip Budapest, how can we use the 3 days otherwise?
Would you recommend spending 1 extra day in Prague and Bled? And keep the 1 day to visit Graz?

Please could you help? Thanks in advance for your help.

These are all wonderful destinations, so I can understand your desire to see them. Nonetheless, your itinerary is, IMO, way too busy. As you note, you'll lose days 4 and 7 to travel, along with a chunk of time getting from Prague to Budapest and from Bled to Vienna. One can see the highlights of Ljubljana in 1 or 1.5 days and the highlights of Bled in a day or 2, but IMO, 2 days is not enough for Budapest and is seriously too little for Vienna. But we all travel for different reasons, so I can't say what will or won't work for you. Good luck!

You can take the night sleeper train from Prague to Budapest. There is one leaving Prague at just slightly after midnight (12:04) and gets into Budapest at 8:35am in the morning. Book a "couchette" in second class in a 4-bunk compartment.

Check out seat61.com for more information on traveling on European trains, or bahn.com for train schedules and even online ticket purchases.

For the Budapest-Ljubljana segment, there are also night sleeper trains, but you will have to change trains in Salzburg. Depart Budapest 19:10 (7:10pm) arrive Salzburg at 1:26am. Depart Salzburg at 1:34am and arrive Ljubljana at 5:58am. This means you have 8 minutes to change trains in Salzburg. The departing track in Salzburg right now is #35. Both are EuroNight trains.

I don't know what kind of passport you have, but generally speaking you don't need a visa if you are just transiting through Croatia. The Croatian border guards will come and check on the passengers, but you just have to show your passport and your train ticket which indicates where you are going.

Graz is a beautiful city but difficult to get to in the mountains, I'd skip Graz this trip.

In Budapest, go to the National Museum, which displays the history of Hungary. Fascinating stuff. Get the audio guide. Tip: the audio guide is rented out by the hour (4 or 6 hour minimum - can't remember exactly), however, you can take it back to the rental desk before your minimal time is up, go and get lunch and then pick up the audio guide after lunch. In other words, your minimal rental time does not have to be continuous. If you go over the minimum time, you have to pay extra per hour.

Have a great trip - sounds exciting!

Budapest is very beautiful place and it is worth a visit. It is better not to miss it. There you can go to the Heroes Square, Fisherman Bastion, the Parliament and make even a Danube boat trip. You won't regret it.