We examined the association between the engagement in regular physical activity (PA) and the academic performance (AP) of school-age children from Santiago Metropolitan Region. In a random sample of 1271 students (13.3 ± 2.3 years old) we measured regular PA, accounting for hours of weekly scheduled exercise, and AP, using national standardized tests scores in Language and Mathematics. Bivariate and multivariate regression analyses were used to model the relation between academic and health-related behaviors. Two outcomes were considered: (i) sufficiency according to the Ministry of Education and (ii) discretionary sufficiency (tests z-scores =50th percentile). About 80% of students were poorly engaged in scheduled exercise (<2 h per week). Devoting more than 4 h per week to scheduled exercise significantly increased the odds of reaching the official and discretionary sufficiency in both Language and Mathematics. Moderate engagement (2–4 h per week) just improved the odds of reaching the discretionary sufficiency standard. These results confirm the poor engagement in regular exercise at the school level. School kids with the highest allocation of time to scheduled exercise have better AP in Language and Mathematics. Our findings support the notion that academic and health-related behaviors are linked and, similarly, that school health programs may have positive effects on educational outcomes