Conservation of marine species is challenging, especially for threatened species that are data deficient, to inform accurate trends and condition of marine populations. The scalloped hammerhead shark (Sphyrna lewini) is classified critically endangered (IUCN), with little to no information on the habitat use and marine park protection of juvenile hammerheads in Queensland. To address this critical knowledge gap, we used sightings and recreational catch information and environmental variables to model (Maxent) the suitable habitat distribution of juvenile scalloped hammerhead sharks across ~11,330 km2 of the Queensland coastline. The study area included three major marine parks (Great Barrier Reef, Great Sandy and Moreton Bay Marine Parks). We used low-level protection (multi-use zones) and high-level protection (“no-take” zones) for suitable habitats within MPAs. Modelling results showed highly suitable habitats accounted for 15.75% of the study area, occurring in nearshore coastal and wetland areas and urban centres. Only 11% of these occurred in no-take MPA zones, while the majority of high suitable habitats occurred in multi-use zones (41.93 %) or outside MPAs (46.98 %). Our results showed most suitable habitats for juvenile scalloped hammerhead sharks do not fall within protected zones in Queensland waters, exposing juvenile sharks to higher anthropogenic pressures, potentially further endangering this species.