Active transportation to school provides a means for youth to incorporate physical activity into their daily routines, and this has obvious benefits for child health. Studies of active transportation have rarely focused on the negative health effects in terms of injury. This cross-sectional study is based on the 2009/10 Canadian Health Behaviour in School-Aged Children survey. A sample of children aged 11–15 years (n=20 076) was studied. Multi-level logistic regression was used to examine associations between walking or bicycling to school and related injury. Regular active transportation to school at larger distances (approximately >1.6 km; 1.0 miles) was associated with higher relative odds of active transportation injury (OR: 1.52; 95% CI 1.08 to 2.15), with a suggestion of a dose–response relationship between longer travel distances and injury (p=0.02). Physical activity interventions for youth should encourage participation in active transportation to school, while also recognising the potential for unintentional injury.