Erosion has reduced the island to sea level and the village now sits on the edge of the extensive Ligitan Reefs.

Kapalai is situated a couple of hours from the east coast of Borneo.

As Kapalai Island is located off the east coast of Sabah / Borneo, Malaysia's easternmost state, direct flights are available to Tawau and Kota Kinabalu on Sabah from Kuala Lumpur on peninsular Malaysia and Singapore.

The closest airport to Kapalai is Tawau, located approximately one hour from Semporna's jetty by minivan.

Many tour operators provide roundtrip transfers from Tawau Airport to Semporna and onward to Kapalai Island.