Birds are the most abundant form of animal life seen on the island. Over 354 species of birds have been recorded. It is a particularly important site for migratory wading birds, which use the area as a resting place during their long flights between southern Australia and their breeding grounds in Siberia.

A species of particular interest is the ground parrot, an endangered species found in the wallum heathlands. Few mammal species are present on the island. The most common are bats, particularly flying foxes. The dingo population on the island is regarded as the most pure strain of dingoes remaining in eastern Australia. Some frog species have specially adapted to survive in this difficult environment. Appropriately called “acid frogs”, these frog species are able to tolerate the acidic condition characteristic of the lakes and swamps on Fraser Island. Other natural inhabitants of the island are possums, sugar gliders, echidnas, swamp wallabies, snakes, lizards and skinks.

The lakes on Fraser Island are poor habitats for fish and other aquatic species because of the purity, acidity and low nutrient levels of the water. Fresh water river turtles are often seen in the lakes.