Wakkanai Station is the northern terminus of the 259.4 km (161.2 mi) Sōya Main Line from Asahikawa.

Previously, it had one island platform and two tracks, but on 30 January 2010, the second track was abolished, and the tracks, switches, departure signals, and in-house signals were removed, and the train stops and rails that were previously used were donated by JR Hokkaido to Wakkanai City, to create a monument in the station square.

The passage from the ticket gate to the platform is a slope, making the station barrier-free.

The station has a Midori no Madoguchi staffed ticket office.

[3] With the privatization of Japanese National Railways (JNR) on 1 April 1987, the station then became under the control of JR Hokkaido.