Yokoate-jima is located 42 kilometres (23 nmi) south-southwest from Takarajima and 60 kilometres (32 nmi) northwest from Amami Ōshima The island is formed by two smaller stratovolcanoes - Higashimine (東峰) to the east, with a maximum elevation of 494.8 metres (1,623 ft) and Nishimine (西峰) to the west, with a maximum elevation of 259 metres (850 ft).

The only known volcanic activity on either peak was towards the end of the Edo period, around 1835 ± 30 years.

The inside of both caldera are forested, whereas the outer slopes of both mountains is largely barren.

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

Kaminonejima (上ノ根島) is another uninhabited island located approximately 2.4 kilometres (1.3 nmi) north of Yokoate-jima.