Kita-Yamagata Station is arranged in a "Y"-shaped configuration. The Ōu Main Line is served by a side platform and one side of an island platform. The other side of the island platform and an additional side platform are used by the Senzan Line. The Aterazawa Line connects to the station with a pair of opposed side platforms at an angle to the station building.
Kita-Yamagata Station opened on 20 July 1921 as a station on the Aterazawa light railway line. Services on the Ōu Main Line began on 11 September 1927 and on the Senzan West Line from 17 October 1933. The station was absorbed into the JR East network upon the privatization of JNR on 1 April 1987.