[3] The structure is located on Mizunokojima, a small rocky island roughly 25 kilometres (16 mi) east-northeast of the city of Saiki, in the middle of the Bungo Channel.

[3] The Mizunokojima Lighthouse began operating on 20 March 1904, after a torturous four-year construction marked by difficulties brought on by the remoteness of the location.

The location had to be abandoned on 4 May 1945 during World War II due to Allied strafing and bombs, but service was restored with acetylene gas lamps by 17 May 1946.

[4] Several typhoons have hit the lighthouse in its years of operation, and the resulting high waves have caused damage.

Keepers' records show that waves taller than the roof of the lighthouse hit on 22 September 1922.