There is evidence that promoting physical activity programs and decreasing sedentary behavior is a potential strategy for improving health-outcomes, peer relationships and social/emotional well-being in at-risk youth. The World Health Organization recommends enhancing physical education and school-based programs with multi-component and evidence-based assessment methodology. In Umbria (Italy) an uncontrolled pilot study project referred to as “Improving Umbrian kids’ healthy lifestyle” was implemented as a systemic school-based intervention directed at 6-year-old primary school children. The intervention applied a consolidated assessment methodology developed by the C.U.R.I.A.Mo. and Eurobis projects that inserted two hours per week of physical education activity into the school curriculum, structured and supervised by specialists with Exercise and Sport Science degrees, for eight months (from October to June) of the school year. We measured anthropometric values (BMI, waist circumference, waist-to-height ratio index) with objective tools. Moreover, we evaluated physical performance variables (speed, strength, and flexibility) using standard tests. Additionally, self-report measures (measured physical activity during the week, sedentary habits, and psychological well-being) were assessed using validated questionnaires. We observed a significant decrease in waist to height ratio, and improvements in physical performance values and self-report questionnaire measures. Our study suggests that the promotion of physical activity in the school setting is likely to result in physically, mentally, and psycho-socially healthier primary-school-age children.