In recent years, children and adolescents have spent more time sitting and engaging in less physical activity than recommended by health authorities. Despite widespread efforts to promote physical activity through school-based programs, the impact of specific intervention programs often remains untested. Therefore, in this pilot study, the effects of a national school-based physical activity program were assessed. A sample of 80 first- and second-grade primary school students aged between 7 and 9 years (M = 7.95, SD = 0.44) of eight classes was cluster randomly assigned to either the experimental group (EG; classroom-based physical activity breaks) or the control group (CG; conventional school lessons). Primary outcomes included objective measurements of sedentary behaviour, step counts, and moderate-to-vigorous physical activity (MVPA) during the intervention. Secondary outcomes encompassed assessments of aerobic fitness performance, executive functions, academic achievement, and scholastic well-being before and after the 20-week intervention. The results indicate that students of the EG spent less time sedentary and took more steps during school mornings than their counterparts of the CG. The physical activity program resulted in a 630-step increase and a 10-minute reduction in sitting time daily. However, there were no effects on MVPA level, aerobic fitness performance, or cognitive functions (including executive functions and academic achievement). The implications of these findings are discussed in light of comprehensive school physical activity approaches.