Background: Evidence of the positive effects of school physical activity (PA) interventions, including classroom-based PA (CBPA), is rapidly growing. However, few studies examine how variations in scheduled PA opportunities and teacher-implemented CBPA affect students’ PA outcomes. Methods: Teachers at 5 elementary schools attended training on how to implement CBPA. Data on school-day PA opportunities [physical education (PE), recess, and CBPA] were obtained via calendar and teacher-recorded CBPA logs. Daily step counts were measured via accelerometry in 1346 students across 65 classrooms in first through fifth grades. Results: PE, recess, and CBPA contributed significantly to students’ daily steps. Males accrued more steps than females over the school day, during PE, and during recess. No gender disparity was seen in the amount of additional steps accrued during CBPA. Overall step counts were lower among fifth-grade students versus first-grade students, but CBPA attenuated this difference such that grade-level differences were not significant in fifth-grade students who received CBPA. Conclusions: Gender disparities in step totals were present on PE and recess days, but not on CBPA days. CBPA appears to provide equal PA benefits for both genders and to potentially minimize the decline in PA among older students.