The station building is a wooden structure of traditional Japanese design with a double tiled roof and has been built and decorated to resemble a Shinto shrine.

South of the station are numerous passing loops, sidings and a turntable, all belonging to a depot on the Hōhi Main Line.

On 2 December 1928, the station was linked up with Tamarai, the western terminus of the Inukai Line (犬飼線), which had been extended westwards in phases from Ōita since 1914.

With the privatization of Japanese National Railways (JNR), the successor of JGR, on 1 April 1987, Miyaji station came under the control of JR Kyushu.

[10] Media related to Miyaji Station at Wikimedia Commons This Kumamoto Prefecture railroad station-related article is a stub.