The purpose of this study was to evaluate the effect of a 2-week overload period immediately followed by a 1-week taper period on the autonomic control of heart rate during the night or after exercise cessation. Eleven male endurance athletes increased their usual training volume by 100% for 2 weeks (overload) and decreased it by 50% for 1 week (taper). A maximal graded exercise test and a constant-speed test at 85% of peak treadmill speed, both followed by a 10-min passive recovery period, were performed at baseline and after each period. Heart rate variability was also measured during a 4-h period in the night or during estimated slow-wave sleep. All participants were considered to be overreached based on performance and physiological and psychological criteria. We found a decrease in cardiac parasympathetic control during slow-wave sleep (HFnu = 61.3% ± 11.7% vs 50.0% ± 10.1%, p < 0.05) but not during the 4-h period, as well as a faster heart rate recovery following the maximal graded exercise test (τ = 61.8 ± 14.5 s vs 54.7 ± 9.0 s, p < 0.05) but not after the constant-speed test, after the overload period. There was a return to baseline for both measures after the taper period. Other indices of cardiac autonomic control were not altered by the overload period. Care should be taken in selecting the most sensitive heart rate measures in the follow-up of athletes, because cardiac autonomic control is not affected uniformly by overload training.