School-based obesity prevention programs are key to promoting healthy habits. The aim of this study was to evaluate the effect of the Planet Nutrition program on BMI z-score and other parameters compared to a control group of Mexican schoolchildren after 9 weeks of intervention. The effect of the summer holidays on the BMI z-score was also evaluated at 23 weeks. A pilot randomized controlled trial design was used and 41 schoolchildren were randomized (21 intervention group and 20 control). The program included 18 nutrition education sessions, 20 physical activity classes and six brochures for parents. At 9 weeks, no significant differences were found between the intervention and control groups in the change in BMI z-score (−0.11, 95% CI −0.23, 0.01). Significant differences were observed in some secondary outcomes: body fat percentage (−1.72, 95% CI −3.42, −0.02), waist circumference (−3.45, 95% CI −5.55, −1.36), physical activity (0.44, 95% CI 0.01, 0.88) and nutrition knowledge (1.15, 95% CI 0.27, 2.03). Summer holidays negatively affected the BMI z-score in both groups, reducing the difference observed between groups at 9 weeks (−0.07, 95% CI −0.22, 0.07). The Planet Nutrition program showed favorable effects in some obesity and lifestyle parameters in the short term.