Background: Globally, disadvantaged populations suffer a high burden of chronic kidney disease (CKD). The trajectory to CKD during childhood and adolescence remains unclear due to a paucity of longitudinal studies. Methods: This was a prospective, population-based cohort study in which since 2002 we have followed 3418 children (1469 non-Aboriginal and 1949 Aboriginal) attending participating schools across New South Wales (NSW), Australia. The albumin:creatinine ratio was measured by dipstick every 2 years together with the body mass index (BMI) and blood pressure. We used multivariable logistic generalised estimating equation models to examine whether Aboriginal children had a higher prevalence of albuminuria compared with non-Aboriginal children with increasing age and to identify potential risk factors. Results: The mean age at enrolment was 10.6 years, at which time 14.2 % of the children were obese and 16.0 % overweight, with 11.5 % found to have albuminuria. Over 8 years (11,387 participant-years) of follow-up the prevalence of albuminuria increased to 18.5 %, overweight to 16.1 % and obesity to 17.2 %. The BMI standard deviation score (SDS) was found to have a differential effect on the risk of albuminuria in Aboriginal and non-Aboriginal children (P interaction < 0.01). The prevalence of albuminuria decreased as the BMI SDS increased in both groups of children, but it increased more in non-Aboriginal children, leading to a 2.5 % higher prevalence of albuminuria in overweight Aboriginal children (95 % confidence interval 1.0–4.2 %). Conclusion: Compared with non-Aboriginal children, Aboriginal children are of higher risk of albuminuria when overweight or obese. We hypothesise that overweight and obesity are key contributors to the development of adult onset CKD among Aboriginal Australians, which needs further exploration in future studies.