Performing high-intensity exercise (HIE) in the morning under sleep deprivation may harm the health benefits related to sufficient sleep and HIE. Therefore, the aim of this study was to explore the effects of acute-partial sleep deprivation on HIE performance and cardiac autonomic activity by monitoring heart rate variability (HRV) indices. Twenty-nine healthy male adolescents in college were recruited to perform a one-time HIE session on the treadmill (Bruce protocol) after ≥7 h of normal control sleep (control) and after ≤4 h of acute-partial sleep deprivation (SD). At the beginning of control and SD periods and after exercising under the two sleep conditions, heart rate (HR), standard deviation of normal to normal (SDNN), square root of the mean squared differences of successive NN intervals (RMSSD), normalized low frequency power (LFn), normalized high frequency power (HFn), number of pairs adjacent NN intervals differing by ≥50 ms in the entire recording count divided by the total number of all NN intervals (pNN50), and short axis and long axis value in Poincaré plot (SD1 and SD2) were measured at rest in an upright sitting position. The participants slept 7.63 ± 0.52 and 3.78 ± 0.69 h during control and SD periods, respectively (p < 0.001). Compared with the control participants, those suffering sleep deprivation experienced a significant decrease in exercise duration, RMSSD, HFn, SD1, and pNN50 as well as a significant increase in maximum heart rate during exercise (p < 0.05). SDNN, RMSSD, HFn, SD1, and pNN50 decreased significantly after exercise (p < 0.05 and 0.01 and 0.001, respectively). In summary, acute-partial sleep deprivation affected aerobic exercise performance the next morning and led to decreased cardiac vagus activity and cardiac autonomic dysfunction.