From 1898, the station was the departure point for the Mellrichstadt–Fladungen railway which ran scheduled services until 1987.

After the reunification of Germany the gap between Bavaria and Thuringia was closed and, after 46 years, Mellrichstadt is once again a through station.

Since 1996 the Fladungen branch has been reactivated as a museum railway, services to all the way through to Mellrichstadt beginning again in 2000.

In 2007, Mellrichstadt was served every two hours by the Mainfranken-Thüringen Express from Würzburg to Erfurt and by the Unterfranken Shuttle from Schweinfurt to Meiningen on the Werra Railway.

That results in what is virtually an hourly service between 5 a.m. and 11 p.m. Mellrichstadt station is also the departure point for numerous bus lines belonging to Omnibusverkehr Franken (OVF) which link up a large part of the Bavarian Rhön, a region of low mountains which extends across the border into Hesse and Thuringia.