A fauna survey of Flinders (Wurriima) and Stanley (Yindayin) Islands in the Great Barrier Reef was conducted in August 2022 to enhance understanding of the islands' fauna and identify management concerns. The survey recorded 72 terrestrial vertebrate species, including 30 species not previously documented in the island group, bringing the total terrestrial vertebrate species count to 118. Notably, the Faint-Striped Blind snake (Anilios broomi) and the Striped-tailed Delma (Delma labialis) were found near or beyond their known distribution limits. Two threatened species were identified: the Endangered Bare-rumped Sheathtail Bat (Saccolaimus saccolaimus nudicluniatus) and the Vulnerable Beach Stone-curlew (Esacus magnirostris) (Queensland Government Nature Conservation Act 1992). Additionally, four Special Least Concern species were recorded: the Lesser Frigatebird (Fregata ariel), Nesting Eastern Osprey (Pandion haliaetus cristatus), Caspian Tern (Hydroprogne caspia), and Crested Tern (Thalasseus bergii). The Near Threatened Coastal Sheathtail Bat (Taphozous australis) was also recorded. Fifty-one voucher specimens or DNA samples were collected to confirm species identities and contribute to taxonomic and population genetic studies. While no species of management concern were detected, the high diversity of limb-reduced lizards and their frequency of occurrence should be considered in fire management planning to ensure the maintenance of adequate refugia. No signs of feral cats, goats, or pigs, previously recorded on the islands, were found during the survey. The introduced Black Rat (Rattus rattus) was present, but its numbers and impacts were deemed low. The species recorded in this survey were comparable to those documented in previous surveys, suggesting that the fauna communities on the islands are likely stable.