Background: Childhood obesity is a major public health concern as it increases the risk of premature death and adult disability. Globally, the latest estimates showed that more than 340 million children and adolescents between the ages of 5 and 19 were overweight or obese in 2016. This study aimed to investigate the disparities in childhood overweight and obesity across 514 districts in Indonesia, based on geographic and socioeconomic factors. Methods: Geospatial and quantitative analyses were performed using the latest Indonesian Basic Health Survey data from 2018. Dependent variables were rates of overweight and obesity among children aged 5–17 years including by gender. Results: This study found that the rates of overweight were 17.2%, 17.6%, and 16.8% among all children, boys, and girls, while the rates of obesity were 7.0%, 7.9%, and 6.1%, respectively. Boys were 1.30 times more likely to be obese than girls, while overweight was similar between both sexes. Urban cities had significantly higher prevalence of childhood overweight and obesity compared with rural districts by up to 1.26 and 1.32 times, respectively. In addition, the most developed region had significantly higher prevalence of childhood overweight and obesity than the least developed region by up to 1.37 and 1.38 times, respectively. With regard to socioeconomic factors, our analysis demonstrated a notable disparity in the prevalence of childhood overweight and obesity across income quintiles. Specifically, the wealthiest districts exhibited a 1.18 times higher prevalence of overweight and obesity among all children compared with the poorest districts. This association was particularly pronounced among boys; in the richest quintile, the prevalence of overweight and obesity was 1.24 and 1.26 times higher, respectively, in comparison to the poorest income quintile. In contrast, district-level education appears to exhibit an inverse relationship with the prevalence of childhood overweight and obesity, although the findings were not statistically significant.