The station is operated by the SBB and is served by Zurich S-Bahn line S9 that provides a half-hourly service between Zürich and Rafz, with alternate trains continuing to Schaffhausen.

[1][2][3] Before the timetable revision in late 2015, the station was served by S-Bahn line S5 from Zurich, and an intermediate stop on the S22 between Bülach and Schaffhausen, which was curtailed from Bülach to Jestetten, in turn it no longer fell under the purview of the ZVV.

Customs checks may be performed aboard trains and in Rafz station by Swiss officials.

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

The collision occurred as the Interregio train, which was running late, was passing through Rafz without stopping.