Fiona Stanley was born in Sydney, New South Wales She loved reading about people like Marie Curie and through her father, who was a researcher on polio, she met Dr Jonas Salk. Stanley has said of her childhood that "in my dreams I would sail out to all the undiscovered islands and inoculate the inhabitants in a whirlwind race to conquer disease and pestilence".
In 1956 the family moved to Western Australia when Stanley's father took the Foundation Chair of Microbiology at the University of Western AustraliaShe went to St Hilda's Anglican School for Girls.
She married Geoffrey Shellam, who later occupied the same Chair of Microbiology. They have two daughters.