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The prevalence of childhood obesity has been increasing worldwide and lifestyle changes are the most important strategies in managing this prevalence. This study aimed to describe the intervention effects of nutrition and physical activities offered as an after school short-term on outcomes of healthy nutrition practices, fitness and lowering fatness. This quasi-experimental study was conducted with a convenience sample of 59 caucasian children, aged 7.7 ± 1.4 years old (52.5% girls) registered on a private school of a middle-size town located in Sao Paulo State, Brazil. The school-based 12-week intervention consisted of 2 weekly 60 minutes section, during 3 months, including a nutritional education and a physical activity curriculum. Anthropometric data was measured for all children at baseline and after 12 weeks. All parents were contacted and requested to complete questionnaire about child’s eating behavior at baseline and after the 12-week program. After the intervention, children showed an increasing in the intake of fruits (64.3%), vegetables (61.9%), and water (52.0%). Overall, 83.3% of the children changed eating behavior according to the questionnaire responded by the parents. Waist circumference was significantly lower and abdominal strength improved after participating in the intervention program. Mean height and weight were significantly higher in boys and girls after a 12-week intervention. Although mean values of BMI remained the same after the intervention it was observed a decreasing in the prevalence of obesity among the children. Thus our study showed that a school-based intervention program focused on nutritional education and physical activity program promoted waist circumference reduction and decreased obesity without affecting the height growth along with improved fitness and healthy eating behavior. This intervention program would be feasible and replicable in others schools around the country.