Flannery was raised in a Catholic family in the Melbourne suburb of Sandringham, close to Port Phillip Bay, where he learned to fish and scuba dive and became aware of marine pollution and its effects on living organisms. He completed a Bachelor of Arts degree in English at La Trobe University in 1977, and then took a change of direction to complete a Master of Science degree in Earth Science at Monash University in 1981. He then left Melbourne for Sydney, enjoying its subtropical climate and species diversity. In 1984, Flannery earned a doctorate at the University of New South Wales in Palaeontology for his work on the evolution of macropods (kangaroos).