This cluster randomized controlled trial (trial-number #) compares effects of two school-based physical activity interventions (aerobic vs. cognitively-engaging) on reading, mathematics, and spelling achievement; and whether effects are influenced by volume of moderate-to-vigorous physical activity and baseline achievement. Twenty-two primary schools participated, where a third and fourth grade class were randomly assigned to the intervention or control group. Intervention groups were randomly assigned to a 14-week aerobic or cognitively-engaging intervention, receiving four physical education lessons a week. Control groups followed their regular physical education program. Academic achievement of 891 children (mean age 9.17 years, 49.4% boys) was assessed with standardized tests before and after the interventions. Post-Test academic achievement did not significantly differ between intervention groups and control group. A higher volume of moderate-to-vigorous physical activity resulted in better post-test mathematics achievement in both intervention groups, and post-test spelling achievement in the cognitively engaging intervention group. Compared to the control group, lower achievers in reading performed better in reading after the cognitively-engaging intervention. A combination of moderate-to-vigorous physical activity and cognitively-engaging exercises seems to have the most beneficial effects. Future intervention studies should take into account quantitative and qualitative aspects of physical activity, and children’s baseline academic achievement.