Infectious diseases contribute a substantial burden of ill-health in Australia’s Aboriginal children. Skin infections have been shown to be common in remote Aboriginal communities, particularly in the Northern Territory, Australia. However, primary care data on skin and other infectious diseases among Aboriginal children living in remote areas of Western Australia are limited. We conducted a retrospective review of clinic presentations of all children aged 0 to 5 years presenting to four clinics located in the Western Desert region of Western Australia between 2007 and 2012 to determine this burden at a local level. Infectious diseases accounted for almost 50% of all clinic presentations. Skin infections (sores, scabies and fungal infections) were the largest proportion (16%), with ear infections (15%) and upper respiratory infections (13%) also high. Skin infections remained high in all age groups; 72% of children presented at least once with skin infections. Scabies accounted for only 2% of all presentations, although one-quarter of children presented during the study for management of scabies. Skin sores accounted for 75% of the overall burden of skin infections. Improved public health measures targeting bacterial skin infections are needed to reduce this high burden of skin infections in Western Australia.