Minami-Nagareyama Station is served by the orbital Musashino Line, which runs between Fuchūhommachi and Tokyo, and by the Tsukuba Express line, which runs from Akihabara in Tokyo and Tsukuba in Ibaraki Prefecture.

The JR East station consists of two elevated opposed side platforms serving two tracks, with a bi-directional centre track used for freight services.

The Tsukuba Express station consists of an underground island platform serving two tracks.

The platforms were approximately 125 m (410 ft) long when built, to accommodate 6-car trains.

The Tsukuba Express platforms were lengthened by 40 m (131 ft) in either direction on 23 September 2012 to allow the train stopping positions to be offset, thus reducing platform crowding during peak periods.