Ellie Gaffney grew up on Thursday Island and went to school at Cowal Creek Mission on Cape York Peninsula. At the start of the Second World War in 1940 her mother and some of her siblings were evacuated to Cherbourg reservation (north west of Brisbane). When her brother was wounded in the war and returned home, the family was allowed to leave Cherbourg and move to Brisbane, and later back to Thursday Island.
Ellie Gaffney decided to become a nurse and received her training in Brisbane. She worked in various hospitals and moved with her husband and daughters to Darwin and later back to Thursday Island, where she had applied for a job at Thursday Island Hospital. When, despite her better qualification, a male white nurse got the job, she gave up her nursing career and took up working in various media organisations and political institutions trying to improve Torres Strait Islander conditions. She was instrumental in the formation of a number of Torres Strait Islander organisations such as Mura Kosker Sorority, the Torres Strait Islander Media Association, and Star of the Sea Home for the Aged.