Aim To study the associations of weather conditions with the travel mode choice for commuting to and from school. Methods A total of 6979 Spanish youths aged 7 to 18 years old (80% adolescents aged 12-18 years old, 51% male) completed a 5-day survey of mode of commuting to school in autumn, winter, and spring. Weather data from the nearest weather station to each school were registered. We used Google Maps (TM) to calculate the distance from home to school. Multilevel logistic regression models were used to estimate odds of active travel based on weather and season. Results We analyzed a total of 163 846 discrete journeys. In winter, children (aged 7 to 11 years old) were less likely to choose an active mode of commuting to school (OR: 0.72, 95% CI: 0.59-0.89, P = 0.003). In spring, adolescents were more likely to choose an active mode of commuting to school (OR: 1.43, 95% CI: 1.19-1.73, P < 0.001). With higher mean temperatures, adolescents were more likely to choose an active mode of commuting from school (OR: 1.02, 95% CI: 1.00-1.04, P = 0.029). Conclusion Certain weather conditions seem to influence the travel mode choice for commuting to and from school in youth, including season and temperature.