[4] The station is jointly owned by the Swiss Federal Railways (SBB CFF FFS) and Deutsche Bahn (DB), and is served by trains of both national operators, as well as trains of the Swiss regional operator Thurbo.

The station is a major intermediate station on the DB's High Rhine Railway that briefly transits Swiss territory on its route along the northern bank of the High Rhine between Basel and Singen.

[5][1] The station is served by long-distance passenger trains running between Zürich and Stuttgart (over the Immendingen–Horb and Horb–Stuttgart lines) and between Basel and Friedrichshafen.

Night bus lines are designated with an "N" followed by the respective route number (almost all are operated by Verkehrsbetriebe Schaffhausen, vbsh).

[13] Schaffhausen is, for customs purposes, a border station for passengers arriving from Germany using direct services without intermediate stops.