It is found in the tropical Indo-Pacific Ocean and normally lives inside the body cavity of a sea cucumber such as the pineapple sea cucumber (Thelenota ananas) or the leopard sea cucumber (Bohadschia argus).
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Two male adult Carapus boraborensis were observed to fight when inside the sea cucumber until one was killed, other fish have been found with bite marks on their tails and one adult was found to have a juvenile silver pearlfish (Encheliophis homei) in its stomach.
There is some competition among Encheliophis homei and another closely related fish Carapus boraborensis for "ownership" of the host sea cucumber, and juvenile E. homei have been found among the stomach contents of C. boraborensis.