It was from the outset planned as a railway junction and was built on land that was then undeveloped to the east of Saalfeld, opposite the old town, with a large area set aside for operations.

In 1874 the Saal Railway was opened from Naumburg via Jena to Saalfeld, giving the city a further rail connection to the northeast.

However, Interzone trains crossed at Saalfeld, as the Franconian Forest Railway, along with the more easterly line via Hof, were the only rail links between East Germany and Bavaria.

In the following years, the station was upgraded to support modern long-distance traffic and received, among other things, three new and fully accessible platforms.

The completion of the Nuremberg–Erfurt high-speed line in 2017 lead to Saalfeld—along with Jena and the Bavarian station of Lichtenfels—losing their ICE stops to Erfurt.