Aim: Physical activity has numerous benefits for children when it comes to academic achievements. This study determined whether active commuting – walking or cycling – to school, as a way of increasing total physical activity levels, was associated with academic Methods: A total of 2138 students participated in the study, which took place in the 2012/ 2013 academic year in three Spanish cities. We used a self-reported questionnaire to assess how the students travelled to and from school and their final school grades. Results: We enrolled 489 primary schoolchildren and 1649 secondary schoolchildren, with similar numbers of boys and girls. The primary schoolchildren who travelled to school by motorbike, car or bus had better grades for all the selected school subjects (p <= 0.009) than those who walked or cycled. No significant associations were found for secondary schoolchildren, except for mathematics and their grade point averages. All models were adjusted for sex, age and school. Conclusion: Active commuting to school was inversely associated with academic achievement in primary school students but not those at secondary school. Longitudinal and intervention studies are needed to further understand our findings.