At Zürich HB, trains of the S16 service usually depart from underground tracks (Gleis) 41–44 (Museumstrasse station).

At the southern end of the service, the S16 is extended to Meilen in the evenings.

The following stations are served:[4][5] As of the December 2022 timetable change,[update] all services are operated with RABe 514 class trains.

[5] Between Zürich Oerlikon and Herrliberg-Feldmeilen, the S16 combines with the S6 to provide a frequency of one train every 15 minutes.

Prior to a change in late 2015, the S16 extended beyond Zürich Flughafen to Effretikon, with alternate trains extended to Thayngen, in the canton of Schaffhausen, running via Winterthur Hauptbahnhof and Schaffhausen.