To present the prevalence and urban-rural differences of overweight and obesity in 7–9-year-old Swedish schoolchildren, we used anthropometric data from a nationally representative survey performed in 2008. Trained staff weighed and measured 4538 children in grades 1 and 2 in 94 primary schools. Weight classification was performed using the IOTF reference and school areas were classified based on level of urbanization and area-level education. Overweight was found in 17% of the children including 3% obese. For overweight, odds-ratios were 1.33 and 1.61 (significant) in semi-urban and rural areas, relative to urban areas. After adjusting for area-level education, differences by degree of urbanisation were greatly attenuated and non-significant. For obesity urban-rural differences were observed in boys only and remained after adjustment for area-level education. For area-level education, risk estimates were significantly elevated and unaffected by urbanization and gender, odds-ratios 1.75 and 2.21 for overweight and 2.62 and 3.69 for obesity, in medium- and low-education areas compared to high-education areas. This supports earlier reports identifying areas with low socioeconomic status as high-risk areas for overweight and obesity. However, this study also suggests that gender should be considered when targeting children in urban as well as rural communities for health promoting interventions.