Sprint interval training involves short bouts of high-intensity exercise and has produced training responses similar to those of endurance training. The effects of multiple supramaximal exercise bouts on neurocardiac modulation have not been examined. Therefore, we investigated the recovery of heart rate (HR) variability and nonlinear HR dynamics in 10 young (20.1 ± 1.2 years) healthy males following single (1) and multiple (4) Wingate tests. HR variability was assessed with time and frequency domain measures, whereas nonlinear HR dynamics were determined by assessing the complexity (sample entropy) and fractal nature (detrended fluctuation analysis) of the HR time series. Responses were determined at pre-exercise baseline and at 3 time points during recovery from exercise: Post1 (5–20 min), Post2 (45–60 min), and Post3 (105–120 min). Following a single Wingate test, all temporal and spectral HR measures had returned to baseline by 1 h of recovery. In contrast, these measures were different from baseline at 2 h following multiple Wingate tests. Fractal HR properties were altered (p < 0.05) at Post1 following a single Wingate test and at Post1 and Post2 following multiple Wingate tests. HR complexity was reduced (p < 0.001) throughout the 2-h recovery following both exercise conditions. In conclusion, Wingate tests result in alterations in cardiac autonomic control, with multiple Wingate tests resulting in larger, more prolonged alterations. Based on the results of the single Wingate test, nonlinear measures, such as HR complexity, may be more sensitive in detecting subtle alterations in neurocardiac behaviour, compared with traditional measures of HR variability.