Background: Complications of scabies and impetigo such as glomerulonephritis and invasive bacterial infection in Australian Aboriginal children remain significant problems and the overall global burden of disease attributable to these skin infections remains high despite the availability of effective treatment. We hypothesised that one factor contributing to this high burden is that skin infection is under-recognised and hence under-treated, in settings where prevalence is high. Methods: We conducted a prospective, cross-sectional study to assess the burden of scabies, impetigo, tinea and pediculosis in children admitted to two regional Australian hospitals from October 2015 to January 2016. A retrospective chart review of patients admitted in November 2014 (mid-point of the prospective data collection in the preceding year) was performed. Prevalence of documented skin infection was compared in the prospective and retrospective population to assess clinician recognition and treatment of skin infections. Results: 158 patients with median age 3.6 years, 74% Aboriginal, were prospectively recruited. 77 patient records were retrospectively reviewed. Scabies (8.2% vs 0.0%, OR N/A, p = 0.006) and impetigo (49.4% vs 19.5%, OR 4.0 (95% confidence interval [CI 2.1–7.7) were more prevalent in the prospective analysis. Skin examination was only documented in 45.5% of cases in the retrospective review. Patients in the prospective analysis were more likely to be prescribed specific treatment for skin infection compared with those in the retrospective review (31.6% vs 5.2%, OR 8.5 (95% CI 2.9–24.4). Conclusions: Scabies and impetigo infections are under-recognised and hence under-treated by clinicians. Improving the recognition and treatment of skin infections by clinicians is a priority to reduce the high burden of skin infection and subsequent sequelae in paediatric populations where scabies and impetigo are endemic.