The effectiveness of the “Extra Fit!” (EF!) education program in promoting healthy diet and physical activity to prevent and reduce overweightness among primary school children aged 9 to 11 was evaluated. A randomized controlled design was carried out in 45 primary schools (n = 1112) in the Netherlands, 23 intervention and 22 control schools. The intervention schools received the education program for two successive school years in grades (U.S. system) 4, 5, and 6 (mean 7.6 h during 16 weeks per school per year). The control schools followed their usual curriculum. No positive effects of EF! were found with regard to behavior and anthropometric measures when follow-up measurements were compared to the baseline. However, from baseline to follow-up after one and two school years, the intervention group improved their knowledge score significantly compared to the control group. Moreover, an effect was observed for mean time spent inactively that increased more in the control group than in the intervention group. In conclusion, limited intervention effects were found for the intervention on knowledge and inactivity. To improve the effectiveness of education programs, we advise focusing on parental involvement, attractive lessons to enlarge the acceptability of the program, and multi-component environmental strategies.