Australia is predicted to have the highest overweight/obesity rate in the world by 2022 outranking the USA and UK. The purpose of this systematic review was to evaluate the associations between childhood obesity and physical and psychological health co-morbidities. Therefore, a systematic literature search was conducted from six databases (2004–2014). Studies were included if they investigated obesity-related co-morbidities with participants residing in Australia aged 0–18 years. Forty-seven studies fulfilled selection criteria. Evidence suggests that overweight/obese Australian children and adolescents, compared to normal-weight peers, had more cardio-metabolic risk factors and higher risk factors of non-alcohol fatty liver disease and were experiencing more negative psychological outcomes (depression, low self-esteem and lower scores of health-related quality of life). Many other health consequences have either not been investigated in Australia, or as frequently as in other countries. Conclusions: Given Australia’s current overweight/obesity prevalence and trajectory, Australia-based studies are needed to identify the suspected co-morbidities, understand the range of individual, social and environmental mechanisms driving obesity, and help identify policies, interventions and strategies that will change the future trajectory and ‘disease burden’ both in Australia and internationally.