Background: Some Canadian schools have modified their daily schedules from the traditional school day (TSD) schedule (two 15-minute breaks and one 60-minute break) to a balanced school day (BSD) schedule (two 40-minute breaks). While this change increases daily planning and instructional time, it also changes the amount of time available for moderate-vigorous physical activity (MVPA). Methods: This study uses a case-control design to examine differences in objectively measured MVPA between children in 3 schools using a BSD schedule and 3 schools using a TSD schedule. Study participants (aged 10-12 years) were recruited from schools in Ontario, Canada. Results: Regardless of schedule type, girls had lower MVPA than boys, and as both boys and girls got older their MVPA significantly decreased. The findings indicate there was no statistically significant difference in the total minutes of in-school MVPA between children from BSD schools and children from TSD schools. MVPA was significantly higher for older girls attending BSD schools than older girls attending TSD schools, suggesting that implementing a BSD may help curb declining MVPA as girls enter adolescence. Conclusion: Despite encouraging findings, more rigorous studies (ie, pre-post experiments with control) are needed to better understand how changing schedules impacts children's health.