The station building is unstaffed and serves only as a waiting room.

The island platform is accessed by a level crossing and ramp.

[2][3][5] Niken'ya Station was opened on 20 April 1913 as an intermediate station on a stretch of track laid down by the Awa National Joint Steamship Company (阿波国共同汽船, Awa-koku kyōdō kisen).

After the company was nationalized in 1 September 1917, Japanese Government Railways (JGR) took over control of the station and operated it as part of the Komatsushima Light Railway and later, the Komatsushima Line.

With the privatization of Japanese National Railways (JNR), the successor of JGR, on 1 April 1987, JR Shikoku took over control of the station.