Background Since 2006 there has been substantial long-term investment in school-based child obesity prevention programs in New South Wales (Australia). Whether these programs have led to population level improvements in children’s weight status and weight-related behaviors are yet to be determined. The purpose of this study was to describe changes in children’s weight status and weight-related behaviors, including Indigenous children, who are at greater risk of poorer health outcomes than non-Indigenous children. Methods Representative cross-sectional population surveys conducted in 2010 and 2015 among children age 5–16 years (n = 15,613). Objective measurements included height, weight, waist circumference, cardiorespiratory fitness, and fundamental movement skills. Indigenous status and indicators of weight-related behavior (i.e., diet, physical activity, school travel, screen-time) were measured by questionnaire with parents responding for children age <10 years and self-report by children age ≥10 years. Results The prevalences of overweight/obesity, obesity and abdominal obesity were higher in 2015, than 2010, and higher among Indigenous than non-Indigenous children at both timepoints. There were some small positive changes towards healthier weight-related behaviors between surveys among all children, but many unhealthy weight-related behaviors remain highly prevalent. The magnitude of changes and the 2015 prevalences of weight-related behaviors were generally similar for Indigenous and non-Indigenous children. Conclusions Schools play an important role in health promotion, but our findings suggest the current approaches need re-thinking. Upstream factors that shape weight-related behaviors such as the regulation of the food industry and food environment, urban, neighborhood and public transport planning must be including in solutions to ensure populations can eat healthily and be physical active.