The station consists of on ground-level island platforms connected to the station building by an underground passage, serving two tracks. The station is unattended.
Nagatori Station opened on 15 December 1953. With the privatization of Japanese National Railways (JNR) on 1 April 1987, the station came under the control of JR East.
Surrounding area
The station is located in an isolated rural area, with few inhabitants. Niigata Prefectural Route 11 is near the station.