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).
On 15 June 2003, traffic on the Basel-Zell line was taken over by SBB GmbH, the German passenger transport subsidiary of Swiss Federal Railways (SBB), and integrated into the network of the Basel Regional S-Bahn.