The station also is served by the Echigo Tokimeki Railway Myōkō Haneuma Line and is located 37.7 kilometers from the starting point of the line at Myōkō-Kōgen and 75.0 kilometers from Nagano.

On the Nihonkai Hisui Line, it is located 59.3 kilometers from the starting point of the line at Ichiburi and 353.8 kilometers from Maibara.

The station has a Midori no Madoguchi staffed ticket office.

[2] 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.

[3] From this date, Naoetsu Station became a boundary station between the Myōkō Haneuma Line (former JR East Shinetsu Main Line) and the Nihonkai Hisui Line (former JR West Hokuriku Main Line) of the Niigata-owned Echigo Tokimeki Railway Company.