The aim of this study was to assess the effects of a 2-year cluster-randomized physical activity and dietary intervention program among 7-year-old (at baseline) elementary school participants on body composition and objectively measured cardiorespiratory fitness. Three pairs of schools were selected and matched, then randomly selected as either an intervention (n = 151) or control school (n = 170). None of the effect sizes of body composition were statistically significant. Children in the intervention group increased their fitness by an average of 0.37 z score units more than the controls (95% CI:-0.27 to 1.01, P = 0.18), representing an improvement of 0.286 W/kg. Boys had higher fitness (mean(diff) = 0.35 z scores, 95% CI: 0.13-0.58, P = 0.001) than girls, independent of study group, fitness z score at baseline and body mass index. Post hoc analysis showed that the intervention school with the highest fitness z score change was significantly different from two of the lowest control schools (mean(diff) = 0.83 z scores, 95% CI: 0.44-1.21, P < 0.0001 and mean(diff) = 0.70 z scores, 95% CI: 0.29-1.10, P = 0.01), but it was also significantly different from the lowest intervention school (mean(diff) = 0.59 z scores, 95% CI: 0.19-0.99, P = 0.05). The results of this intervention are inconclusive as regards to the effects on fitness, but the intervention did not have any statistically significant effect on body composition.