Evidence-based profiling of obesity and overweight in Indigenous Australian children has been poor. This study systematically reviewed evidence of the prevalence and patterns of obesity/overweight, with respect to gender, age, remoteness and birth weight, in Indigenous Australian children, 0–18 years (PROSPERO CRD42014007626). Study quality and risk of bias were assessed. 25 publications (21 studies) met inclusion criteria, with large variations in prevalence for obesity or overweight (11% to 54%) reported. A high degree of heterogeneity in study design was observed, few studies (6/21) were representative of the target population, and few appropriately recruited Indigenous children (8/21). Variability in study design, conduct and small sample sizes mean that it is not possible to derive a single estimate for prevalence although two high-quality studies indicate at least one in four Indigenous Australian children are overweight or obese. Four of six studies reporting on gender, found overweight/obesity higher in girls and eight studies reporting on overweight/obesity by age suggest prevalence increases with age with one high quality large national study reporting total overweight/obesity as 22.4% of children aged 2–4 years, 27.5% of those aged 5–9, 38.5% aged 10–14 and 36.3% aged 15–17. Three of four studies, reporting obesity/overweight by region, found lower rates for children living in more remote areas than urban areas.