The station is on the ground level with two opposing side platforms for two tracks, plus two sidings on the Isahaya side. The platforms are connected by a level crossing within the premises. When trains are not switching, both up and down trains stop at the platform on the station building side. As Isahaya Station only has one platform and one track, the siding is used for storing vehicles. There is a two-story station building on the north side of the platform. It The station is staffed. There is an automatic ticket machine in the waiting room inside the station building.[1][2]
^ abcKawashima, Ryōzō (2013). 図説: 日本の鉄道 四国・九州ライン 全線・全駅・全配線・第5巻 長崎 佐賀 エリア [Japan Railways Illustrated. Shikoku and Kyushu. All lines, all stations, all track layouts. Volume 5 Nagasaki Saga area] (in Japanese). Kodansha. pp. 22, 67. ISBN9784062951647.
^ ab"本諫早駅" [Hon-Isahaya Station]. hacchi-no-he.net. Retrieved 16 March 2018.
^"第67版(令和2年)長崎県統計年鑑" [Nagasaki Prefecture Statistics Yearbook 67th Edition]. Nagasaki Prefectural Government website. Retrieved 16 March 2024. See table at section under Transportation and Communications.