Kakunodate Station consists of a single side platform and an island platform serving the JR portion of the station, and a single side platform for the Akita Nairuke Railway. The station building, designed to resemble a samurai residence, was selected to be one of the Hundred Stations of Tohoku.
Kakunodate Station opened on July 30, 1921 as a station on the Obonai Railway, which was nationalized into the Japanese Government Railways (JGR) the following year. The JGR became Japan National Railways (JNR) after World War II. The Kakunodate Line (which later became the Akita Nairiku Railway) began operation from November 1, 1971.. The station was absorbed into the JR East network upon the privatization of the JNR on April 1, 1987. Services on the Akita Shinkansen began on March 22, 1997.