Bahnstrecke Halle–Bebra
Mühlhausen was connected to a railway the first time in 1870 with the opening of the Gotha–Leinefelde line of the Thuringian Railway Company (). A junction station was added to the existing through station in 1897 for the opening of the light railway to Ebeleben by the Mühlhausen-Ebeleben Railway Company ("Eisenbahn-Gesellschaft Mühlhausen-Ebeleben", MEE). The Mühlhausen Tramway opened its first line from the station forecourt in 1898. The station was rebuilt with the opening of the line to Treffurt in 1911 and the MEE station was integrated with the former Thuringian Railway Company station, by then part of the Prussian state railways.