It is located east of the centre of Mühlhausen in the valley of the Unstrut.

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.

In 1969 the tramway was shut down and in the same year freight transport also ended on the last remaining remnant of the line to Treffurt, which was partly closed after the Second World War due to the establishment of the Inner German border Treffurt.

In the 2016 timetable Mühlhausen (Thür) station was served by the following lines: