Health benefits of physical activity are well known, yet available physical activity data is limited from children living in African and Asian countries. The purpose of the cross-sectional study was to evaluate and compare physical activity and sedentary behavior patterns, particularly hourly variations, among children in Kenya and Japan. Participants included 298 primary school students (122 Kenyan, 176 Japanese) aged 9–12 years. Physical activity and sedentary behavior were measured with accelerometers. Domain-specific physical activity, screen time, and proportion of children using active transport to school were measured by questionnaire. A two-way ANOVA (countries × time) was used to examine the differences in the activity patterns between Kenyan and Japanese children. The results from the present study demonstrated that Kenyan children spent more time in moderate-to-vigorous physical activity compared to Japanese children (p < 0.05) with the greatest differences found for weekday evenings (for boys and girls) and weekend afternoons (for girls). This suggests that these were ‘critical periods’ to differentiate the physical activity levels between Kenyan and Japanese children. However, a higher proportion of the children from Japan used active transport to school and spent less time in television viewing and computer gaming. The results suggest that both countries have successes and challenges that can aid in developing effective and country-specific intervention strategies for promoting physical activity.