Minami-Wakkanai Station is served by the 259.4 km (161.2 mi) Sōya Main Line from Asahikawa to Wakkanai, and lies 256.7 km from the starting point of the line at Asahikawa.

[3] Sōya and Sarobetsu limited express trains stop at this station.

On 25 June 1924 the track between this station and Kabutonuma on the Teshio Kita Line opened.

[3] On 6 November 1952 the station was relocated, moving approximately 1 one kilometer from Wakkanai city center to near the junction of the Soya Main Line and Tempoku Line.

With the privatization of Japanese National Railways (JNR) on 1 April 1987, the station came under the control of JR Hokkaido.