Apunipima Cape York Health Council emerged out of a health conference held at Pajinka Wilderness Lodge, near Injinoo, in 1994. The conference was attended by representatives of 17 Cape York communities and associated homelands concerned about poor health status of Cape York Aboriginal and Torres Strait Islanders.

Apunipima was officially established on 14 September 1994 as a health advocacy organisation, mandated to inform the Cape York Land Council and the ATSIC Regional Council about health issues on Cape York.

In the two decades since its inception Apunipima has grown from a small advocacy organisation to the largest Aboriginal Community Controlled Health Organisation in Queensland.