The station consists of two opposed side platforms located inside the 11,353 meters (37,247 ft) long Kubiki Tunnel, 40 meters (130 ft) below ground, connected to the entrance gate by 290 steps.

Due to the air pressure generated by passing trains, access to the platform is limited and a protected waiting room with heavy metal doors keep passengers safe from typhoon-like wind.

[1] The station opened on December 16, 1912, as part of the Japanese Government Railways (JGR, JNR after 1949).

From 14 March 2015, with the opening of the Hokuriku Shinkansen extension from Nagano to Kanazawa, local passenger operations over sections of the Shinetsu Main Line and Hokuriku Main Line running roughly parallel to the new Shinkansen line were reassigned to third-sector railway operating companies.

[2] From this date, Tsutsuishi Station was transferred to the ownership of the third-sector operating company Echigo Tokimeki Railway.