High-intensity interval training (HIIT) improves traditional cardiovascular disease (CVD) risk factors in adolescents, but no study has identified the influence of HIIT on endothelial and autonomic function in this group. Thirteen 13- to 14-yr-old adolescents (6 girls) completed six HIIT sessions over 2 wk. Each training session consisted of eight to ten 1-min repetitions of cycling at 90% peak power interspersed with 75 s of unloaded cycling. Traditional (triglycerides, cholesterol, glucose, insulin, and blood pressure) and novel [flow-mediated dilation (FMD), heart rate variability (HRV)] CVD risk factors were assessed in a fasted and postprandial state before (PRE), 1 day after (POST-1D), and 3 days after (POST-3D) training. Aerobic fitness was determined PRE and POST-3D. Two weeks of HIIT had no effect on aerobic fitness or traditional CVD risk factors determined in the fasted or postprandial state (P > 0.15). Compared with PRE, fasted FMD was improved POST-1D [P = 0.003, effect size (ES) = 0.70] but not POST-3D (P = 0.32, ES = 0.22). Fasted FMD was greater POST-1D compared with POST-3D (P = 0.04, ES = 0.48). Compared with PRE, postprandial FMD was greater POST-1D (P < 0.001, ES = 1.01) and POST-3D (P = 0.01, ES = 0.60). Fasted HRV was greater POST-1D (P = 0.001, ES = 0.71) and POST-3D (P = 0.02, ES = 0.44). The test meal lowered HRV in all laboratory visits (P < 0.001, ES = 0.59), but there were no differences in postprandial HRV between visits (P > 0.32 for all). Two weeks of HIIT enhanced endothelial function and HRV without improvements in traditional CVD risk factors. However, most of this favorable adaptation was lost POST-3D, suggesting that regularly performing high-intensity exercise is needed to maintain these benefits.