Isahaya station is a main station of city of Isahaya, the third most populous city in Nagasaki prefecture, after prefectural capital Nagasaki and Sasebo. Isahaya station is a joint-use station for JR Kyushu and Shimabara Railroad. Isahaya station itself has more daily ridership than Sasebo station, which makes Isahaya station as the second busiest station in Nagasaki prefecture.
Isahaya station serves for JR Nagasaki main line, JR Omura line and Shimabara Railroad line. All trains call at Isahaya station. Limited express Kamome which connects main station of biggest city in Kyushu, Fukuoka's Hakata station and Nagasaki station. JR Omura line's rapid train, Seaside liner connects Nagasaki and Sasebo. Shimabara Railroad connects Isahaya and Shimabarako station in Shimabara city which is located on the southeast part of Shimabara peninsular.
Not only limited express Kamome, there are certain local trains connecting Nagasaki station but be aware when taking local train to Nagasaki. Nagasaki main line has two separate tracks between Kikitsu and Urakami stations. The original one, which takes longer to reach Nagasaki is nominally called Nagayo line due to passing Nagayo station. The newer and shorter one which passes Ichinuno station is now the main track of Nagasaki main line, which makes Nagayo line as the feeder line. Limited express Kamome and Rapid Seaside Liner run via Nagayo. Local trains which run on Nagayo line is mentioned as VIA NAGAYO and on the other hand, train stops at Ichinuno is mentioned as VIA ICHINUNO.