The station is 171.64 metres above sea level and was opened on 29 June 1876 simultaneously with the railway.

The station building was renovated in 2000 and attracted some retail outlets (shops selling magazines, flowers and model trains and several snack bars).

In 1878 the first siding was established, which was followed by another one in 1889 and by one to Schott & Gen., now Jena Glass Company (JENAer Glas), in 1894.

There was also a brewery connection, on which wagons (mostly carrying coal) were moved up to the terminal and were then transferred to a light railway with 600 mm gauge.

It is the busiest of the Jena stations and it is currently used on average by about 5,000 passengers a day, so its ridership is higher than that of Jena Paradies station, which is an Intercity-Express stop on the Saale Railway, but has a comparatively low 3,500 passengers a day.

Jena West station is heavily frequented by commuters and students on their way to the neighbouring cities of Erfurt and Weimar, which are about 30 and 15 minutes away respectively.