Cardiovascular disease and type 2 diabetes mellitus are leading contributors to the health inequity experienced by Aboriginal and Torres Strait Islander peoples, and their antecedents can be identified from early childhood. We aimed to establish the quality of available data and the prevalence of cardiometabolic risk markers among Aboriginal and Torres Strait Islander children and youths (0–24-year-olds) to inform public health approaches. A systematic review of the peer-reviewed and grey literature was conducted between 1 January 2000–28 February 2021. Included studies reported population prevalence of cardiometabolic risks, including elevated blood pressure, obesity, central adiposity, dyslipidaemia, hyperglycaemia, and ‘metabolic syndrome’ for Aboriginal and Torres Strait Islander people aged 0–24 years. Fifteen studies provided population estimates. Data quality was limited by low response rates (10/15 studies) and suboptimal outcome measurements. Obesity is the most reported risk (13/15 studies). Aboriginal and Torres Strait Islander children have an excess risk of obesity from early childhood and prevalence increases with age: 32.1% of Aboriginal and Torres Strait Islander 18–24-year-olds had obesity and 50.8% had central adiposity. In a cohort of 486 9–14-year-olds in Darwin, 70% had ≥1 component of metabolic syndrome; 14% met the full criteria for the syndrome. The prevalence of cardiometabolic risk in Aboriginal and Torres Strait Islander young people is difficult to estimate due to limitations in measurement quality and sampling representativeness. Available data suggest that cardiometabolic risk markers are evident from early childhood. The establishment of national and state-level datasets and a core outcome set for cardiometabolic screening would provide opportunities for preventative action.