Background: Classroom Active Breaks (CABs), short active sessions integrated in the school time, have been recognized as a promising tool to reduce sedentary behavior and increase Physical Activity (PA) levels in children. “AulAttiva” is a six-month CABs-based program implemented in primary schools of the province of Naples. The aim of this study was to evaluate its effectiveness by comparing PA and sedentary time of participating pupils respect to a control group, considering also their weight status. Methods: Four third-grade classes, each from 4 schools out of 32 participating in AulAttiva, and 4 third-grade classes, each from 4 schools out of 74 that did not take part, were randomly selected. Finally, 58 children composed the intervention group and 57 the control group. Age, gender, weight and height were registered for each participant. Weight status was classified as non-overweight and overweight/obesity. Sedentary time and PA were assessed through accelerometers along a school day. Results: Light PA was 4 min higher in the AulAttiva group with respect to controls (p = 0.046). Within the non-overweight children, the AulAttiva group spent less time in sedentary behavior and more time in light and total PA than controls. No significant differences were found between the overweight/obese subgroups. Conclusions: The results support the effectiveness of CABs in increasing PA during the school day. Greater effects were registered among normal weight pupils, suggesting the possible influence of weight status on children’s participation to the intervention. Further studies are needed to improve the compliance of overweight/obese children to this intervention.