The station consists of one ground-level island platform connected to the station building by a footbridge, serving two tracks, located adjacent to the elevated Joetsu Shinkansen tracks. The station is unattended.
The station opened on 1 November 1915 as Jōoka Station (城岡駅?). It was renamed Kita-Nagaoka on 20 June 1951. With the privatization of Japanese National Railways (JNR) on 1 April 1987, the station came under the control of JR East. A new station building was completed in July 2014.