The prevalence of childhood overweight and obesity has been shown to differ among regions, including rural-urban regional differences within nations. This study obtained simultaneous accelerometry-derived physical activity, 24 h activity, and food records to clarify the potential contributing factors to rural-urban differences in childhood overweight and obesity in Japan. Sixth-grade children (n = 227, 11-12 years old) from two urban elementary schools in Kyoto and four rural elementary schools in Tohoku participated in the study. The children were instructed to wear a pedometer that included a uniaxial accelerometer and, assisted by their parents, keep minute-by-minute 24 h activity and food records. For 12 children, the total energy expenditure was measured by the doubly labeled water method that was used to correct the Lifecorder-predicted activity energy expenditure and physical activity level. The overweight and obesity prevalence was significantly higher in rural than in urban children. The number of steps per day, activity energy expenditure, physical activity level, and duration of walking to school were significantly lower in rural than in urban children. In contrast, the reported energy intake did not differ significantly between the regions. The physical activity and duration of the walk to school were significantly correlated with body mass index. Rural children had a higher prevalence of overweight and obesity, and this may be at least partly caused by lower physical activity, especially less time spent walking to school, than urban children.