Kiyosato Station serves as the gateway to the surrounding highland resort area as well as the Kiyosato Educational Experiment Program (KEEP), a Summer camp, agricultural training and conference center established in 1938 by American missionary Paul Rusch.

The station consists of two ground-level opposed side platforms, connected by a level crossing.

The station has a Midori no Madoguchi staffed ticket office.

Kiyosato Station was opened on 27 July 1933 by the Japanese Government Railways.

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