The station is located on both the Wallisellen to Rapperswil via Uster and Effretikon to Hinwil railway lines, which converge at junctions to the north and south of the station.

It became a junction station in 1876, when the Effretikon to Hinwil line opened.

In 1903, Wetzikon station also became the interchange point with the Wetzikon-Meilen-Bahn (WMB), a newly built metre gauge electric tramway that linked the area with Meilen on the shores of Lake Zürich.

The WMB originally ran beyond Meilen station, to terminate at Kempten, but this section closed in 1939 leaving the station as the line's terminus.

[2] During weekends, there is also a nighttime S-Bahn service (SN5) offered by ZVV.