After the opening of the line between Basel and Schopfheim in 1862 by the Wiese Valley Railway Company (Wiesenthalbahn-Gesellschaft) from the Badischen Bahnhof (Baden station) in Basel, the line was extended to Zell on 5 June 1876 by the Schopfheim-Zell Railway Company (Schopfheim-Zeller Eisenbahn-Gesellschaft).

The entrance building of Zell station is now privately owned and is no longer used for railway purposes.

Since the incorporation of the Wiese Valley Railway in the Basel Regional S-Bahn, Zell station has only had a single track with a platform next to the entrance building.

Directly in front of the platform next to the entrance building there are two bus stops, which are served by buses to the surrounding communities, including along the former railway line to Todtnau.

The transitional fares of Tarifverbund Nordwestschweiz (Tariff association of Northwestern Switzerland, TNW) are honoured in Basel.