To investigate the effects of supramaximal high-intensity interval training (SIT) vs functional high-intensity interval training (FIT) on sports performance, oxidative stress, and acute and chronic flow-mediated dilatation (FMD) were observed. Forty-five young male athletes were randomly allocated to control (CON), SIT, and FIT groups. The SIT program consisted of 10 sets of 30 s of cycle ergometry at 170 % of VO2peak alternating with 30 s rest periods. The FIT program consisted of 10 training postures of 30 s alternating with 30 s rest periods, matching the SIT in energy expenditure and duration of training session. Both SIT and FIT groups underwent training 3 times per week for 10 weeks. Maximal oxygen consumption increased significantly in both SIT and FIT groups relative to pre-test status and the CON group (P<0.05), while the height of counter movement jump increased only in the FIT group. FMD increased significantly with 10 weeks of training in both groups relative to pre-test and the CON group. Only the FIT group had increased FMD at 5 min after training in post-test (P<0.05). Plasma malondialdehyde decreased significantly only in the FIT group (P<0.05). In conclusion, both SIT and FIT programs exerted beneficial effects on health-related physical fitness and FMD. However, the FIT program generated superior results in counter movement jump and acute FMD.