Background While there have been several school‐based physical activity (PA) interventions targeting improvement in cardiovascular disease (CVD) risk factors, few have assessed long‐term effects. The aim of this paper was therefore to determine intervention effects on CVD risk factors 5 years after cessation. Methods Two schools were assigned to intervention (n = 125) or control (n = 134). The intervention school offered 210 min/week more PA than the control school over two consecutive years (fourth and fifth grades). Follow‐up assessment was conducted 5‐year post‐intervention (10th grade) where 180–210 (73%–85%) children provided valid data. Outcomes were CVD risk factors: triglyceride, total‐to‐high‐density‐lipoprotein‐cholesterol ratio (TC:HDL ratio), insulin resistance, blood pressure (BP), waist circumference, and cardiorespiratory fitness (VO2peak). Variables were analyzed individually and as a composite score through linear mixed models, including random intercepts for children. Results Analyses revealed significant sustained 5‐year intervention effects for HDL (effect sizes ES = 0.22), diastolic BP (ES = 0.48), VO2peak (ES = 0.29), and composite risk score (ES = 0.38). These effects were similar to the immediate results following the intervention. In contrast, while TC:HDL ratio initially decreased post‐intervention (ES = 0.27), this decrease was not maintained at 5‐year follow‐up (ES = 0.09), whereas WC was initially unchanged post‐intervention (ES = 0.02), but decreased at 5‐year follow‐up (ES = 0.44). Conclusion The significant effects of a 2‐year school‐based PA intervention remained for CVD risk factors 5 years after cessation of the intervention. As cardiometabolic health can be maintained long‐term after school‐based PA, this paper demonstrates the sustainability and potential of schools in the primary prevention of future CVD risk in children.