Although the station is in Switzerland, it is located on the Deutsche Bahn's High Rhine Railway that links Basel to Singen.

[5] Thanyngen is, for customs purposes, a border station for passengers arriving from Germany.

Customs checks may be performed in the station or on board trains by Swiss officials.

Systematic passport controls were abolished when Switzerland joined the Schengen Area in 2008.

[6][7] As of the December 2022 timetable change,[update] the following S-Bahn services stop at Thayngen station:[8][9]