Abstract Scabies is estimated to affect 455 million people worldwide and is one of 20 neglected tropical diseases recognized by the World Health Organization (WHO). It is caused by a parasitic mite infestation that is hyperendemic in low-resource regions, and the disease burden in northern Australia is believed to be among the highest in the world. However, few recent prevalence assessments have been conducted in northern Australia and it is not known whether historical assessments are still representative of the disease burden. Therefore, it is difficult to advocate for the allocation of government funding and resources without accurate information on the burden of disease. Considering the effectiveness of an ivermectin-based mass drug administration (MDA) treatment programme in northern Australia is important to explore a control strategy, following successful large trials conducted in the Pacific and recommendations from the WHO. The aim was to consider the burden of scabies and other skin conditions in an indigenous community in northern Australia, from undertaking a simplified skin assessment of all consenting community residents. An observational cross-sectional study design was used for this purpose. Five field teams covered different regions in Maningrida. The teams were comprised of a medical practitioner from the investigative team who worked alongside a local healthcare worker and an Aboriginal healthcare worker. All community residents who gave verbal consent were administered ivermectin, or topical permethrin cream if ivermectin was contraindicated, as part of a MDA programme, which was locally developed and implemented by the Mala’la Health Service. Simplified skin examinations (n = 1306) were conducted in Maningrida during Healthy Skin Week from 14 to 18 November 2022, with verbal consent from 99% of community residents approached for recruitment to undergo a simplified skin assessment and administration of ivermectin as part of the MDA treatment programme. The point prevalence for scabies was 25.2% (330 individuals). Ninety-three people (7.1%) were diagnosed with impetigo, and ∼40% of community residents had evidence of skin disease. No study participants were diagnosed with crusted scabies. Scabies is endemic in indigenous communities in northern Australia. This was the first prevalence assessment to be conducted in the Northern Territory since the East Arnhem Healthy Skin Project, which concluded in 2007, and the first MDA treatment programme conducted by an aboriginal medical service as a local health intervention. The consideration of effective rapid mapping and regional control strategies is essential to tailor a public health response that addresses the high burden of skin disease in northern Australia.