This study analyze the relation between body composition, physical activity (PA), and sex in Chilean children from rural and urban public educational institutions. The prevalence of obesity (according to BMI) was 30.88% in urban children and 28.93% in rural children. Central obesity presented mainly in the rural girls. Approximately 90% of the participants reported <7 h of PA/week, regardless of residential area. In addition, central fat was strongly associated with rural residence; the children reported lower PA levels, and they presented a higher prevalence of central fat. The results reflect the need to implement programs to improve PA conditions in the child urban-rural population.