What is the best way to get from Thessoloniki, Greece to Dubrovnik

I can't answer your question but I thought you should know that there are no trains passing from Greece into another country, or in the reverse direction for that matter. I suppose it might be possible to take a train from Thessaloniki to a town close to the border and then a bus across the border and then another train the rest of the way, but this is something you'll have to find out for yourself.

Flying may be your best bet. Use Skyscanner to check your options. When I just popped in a random date I found some options. They're not easy (require one or two transfers) but are doable. If you are interested in seeing Zagreb, you can fly there (still typically need a transfer - flights aren't direct). For example, on the date I was looking at you can go from Thessa to Zagreb via Istanbul on Turkish Airlines for $265.

I will be traveling in the Balkans next May-June and from I can tell, there is no easy overland route linking these two. It seems to be a time-consuming affair that combines buses, minivans, etc., linking a chain of stops on the way (more than one route possible). If you have 2 or 3 days available to do this, then it can be cobbled together.

I would fly it.

Thanks for your ideas. A great help. Jo