Myōkō-Kōgen forms the boundary station between the 37.3 km Shinano Railway Kita-Shinano Line from Nagano and the 37.7 km Echigo Tokimeki Railway Myōkō Haneuma Line to Naoetsu.

No regularly scheduled through-running services operate, but a cross-platform transfer is provided, with Shinano Railway trains normally using platform 2 and Echigo Tokimeki Railway trains normally using platform 3.

[3] With the privatization of JNR on 1 April 1987, the station came under the control of East Japan Railway Company (JR East).

[3] 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 running roughly parallel to the new shinkansen line were reassigned to different third-sector railway operating companies.

[2] From this date, Myōkō-Kōgen Station became a boundary station between the Shinano Railway Kita-Shinano Line of Nagano Prefecture to the south and the Echigo Tokimeki Railway Myōkō Haneuma Line of Niigata Prefecture to the north.