BACKGROUND: This randomised controlled trial (RCT) assessed the effect of a 1-year, partially supervised, physical activity (PA) intervention on a cardiovascular disease (CVD) risk score in adult survivors of childhood cancer. METHODS: We included childhood cancer survivors ≥16 y at enrolment, <16 y at diagnosis and ≥5 y in remission. The intervention group was asked to perform an additional ≥2.5 h of intense physical activity/week, controls continued exercise as usual; assessments were performed at baseline, 6 months (T6) and 12 months (T12). The primary endpoint was change in a CVD risk score (average z-score of waist circumference, blood pressure, fasting glucose, inverted high-density lipoprotein cholesterol, triglycerides, and inverted cardiorespiratory fitness) from baseline to T12. We performed intention-to-treat (ITT, primary) and 3 per protocol analyses. RESULTS: We randomised 151 survivors (44% females, 30.4 ± 8.6 years). We found a significant and robust reduction of the CVD risk score in the intervention compared to the control group at T6 and T12 across all analyses; with a difference in the reduction of the CVD risk z-score of -0.18 (95% confidence interval -0.29 to -0.06, P = 0.003) at T12 in favour of the intervention group (ITT analysis). CONCLUSIONS: This RCT showed that a long-term PA intervention can reduce CVD risk in long-term survivors of childhood cancer. TRIAL REGISTRATION: Clinicaltrials.gov: NCT02730767.