Integrating physical activity into the curriculum has potential health and cognitive benefits in primary school children. The aim of this study was to investigate the effects of physically active academic lessons on cardiovascular fitness, muscular fitness and executive functions. In the current randomized controlled trial, 499 second and third graders within 12 primary schools (mean age = 8.1 ± 0.7) were randomized to the intervention (n = 249) or control condition (n = 250). The physically active academic lessons were given for 2 consecutive school years, 22 weeks per year, three times a week, with a duration of 20-30 min per lesson. Multiple tests were administered before, between and after the intervention period, measuring cardiovascular fitness, muscular fitness and executive functions. Multilevel analysis accounted for the nested structure of the children within classes and schools. Results showed a larger improvement in speed-coordination (B = -0.70, P = 0.002) and a lower improvement in static strength (B = -0.92, P < 0.001) for the intervention group compared with the control group. The current lessons did not result in a significant change in executive functions.