OBJECTIVES: This study aimed to determine the effect of classroom-based physically active lessons on time on task (TOT) and the relationship of TOT with academic achievement controlling for key demographic variables. METHODS: Seventeen elementary schools were cluster randomized to receive classroom physical activity (Academic Achievement and Physical Activity Across the Curriculum, n = 9) or control (i.e., no physical activity, n = 8) for a 3-yr trial. Teachers were trained to deliver physically active lessons with moderate to vigorous intensity targeting 100 min·wk. Outcome measures included academic achievement (Wechsler Individual Achievement Test III), administered at baseline and repeated each spring for 3 yr; time spent in moderate to vigorous physical activity (MVPA); and TOT pre- and postphysical activity. Multilevel modeling was used to estimate the effects of percent time spent in MVPA and percent TOT postlesson on academic achievement and the change in these effects over 3 yr, accounting for dependency among observations and covariates including age, gender, race, free or reduced lunch, BMI, and fitness. RESULTS: A greater percentage of time performing MVPA was significantly associated with higher math scores (P = 0.034) and spelling scores (P < 0.001), but not reading scores. Academic achievement was not associated with TOT. CONCLUSION: Findings suggest that a greater percentage of time spent participating in MVPA results in higher math scores and spelling scores, but not reading scores, independent of TOT. Future studies should continue to evaluate the influence of physically active classroom lessons on time spent on task and its effect on academic achievement. Furthermore, strategies are needed to maximize the effect and to determine the sustainability of physical activity’s effect on classroom behavior and academic achievement.