The aims of this study were to investigate in adolescents: 1) the relationships of physical activity (PA) and cardiorespiratory fitness (CRF) to traditional CVD risk factors, rest and recovery autonomic function; and 2) whether autonomic function strengthens the associations between PA, CRF and CVD risk. Fifty-four (22 girls) adolescents had traditional CVD risk factors, rest and recovery autonomic function evaluated. CRF was measured using a steep ramp cycle test and PA was assessed with accelerometers. Resting HRV (and RMSSD(30)) and heart rate recovery (T(30), HHRtau) were used. Clustered traditional (CVDR(trad)) and autonomic (CVDR(auto)) risk scores were created and added to form a composite clustered CVD risk score (CVDR(com)). PA and CRF were significantly and negatively associated with traditional CVD risk factors. Moderate (MPA) and vigorous (VPA) were positively related to resting RMSSD, and negatively related to T(30) and HHRtau (all P<0.05). RMSSD(30) recovered faster in the high compared to low median split for VPA. Stronger associations for CVDR(com) compared to CVDR(trad) were observed for MPA (CVDR(com): r(2)=0.32, P=<0.001; CVDR(trad): r(2)=0.17, P=0.002), and VPA (CVDR(com): r(2)=0.18, P=0.001; CVDR(trad): r(2)=0.06, P=0.08). These findings strengthen the proposed additional beneficial effects of PA on autonomic function above traditional CVD risk factors.