Kogajajima is located 5.6 kilometres (3.0 nmi) east-southeast from Gajajima.

It is the partial exposed portion of an eroded lava dome of a stratovolcano arising from the ocean floor, to a maximum height of 301 metres (988 ft) above sea level.

No volcanic activity has been recorded in historic times.

The local climate is classified as subtropical, with a rainy season from May through September.

In 1896, the island was transferred to the administrative control of Ōshima District, Kagoshima, and from 1911 was administered as part of the village of Toshima, Kagoshima.