The company boundary between JR West and JR Kyushu is at the west end of this station where there is an entrance signal from Moji, and trains on the San'yō Main Line past this station are under the control of the Kyushu Railway Company (JR Kyushu) The station consists of two raised island platforms connected to a mezzanine level of the station building by the stairs/escalator near the north end of each platform.

Shimonoseki Station opened on 27 May 1901 as Bakan Station (馬関駅) on the San'yō Railway about 700 meters east from its current location, but adjacent to the Kanmon Renrakusen (関門連絡船, Shimonoseki Moji Railway Ferry) .

San'yō Railway ferry operations to Korea began from 11 September 1905.

On 29 September 1999, the Shimonoseki Station massacre occurred, with five deaths with ten injuries.

On 7 January 2006, the main station building was destroyed by fire and a 74-year-old man was arrested for arson.