OBJECTIVE: Most studies investigating the effects of non-pharmacological interventions, such as physical training (PT), on cardiac autonomic control, assessed the HRV only in resting conditions. Recently, a new time-frequency mathematical approach based on the short-time Fourier transform (STFT) method has been validated for the assessment of HRV in non-stationary conditions such as the immediate post-exercise period. The aim of this study was to evaluate the effects of the PT on post-exercise cardiac autonomic control using the time-frequency STFT analysis of the HRV. METHODS: Twenty-one healthy male volunteers participated in this study. The subjects were initially evaluated for their physical exercise/sport practice and allocated to groups of low physical training ((Low)PT, n = 13) or high physical training (H(igh)PT, n = 8). The post-exercise HRV was assessed by the STFT method, which provides the analysis of dynamic changes in the power of the low- and high-frequency spectral components (LF and HF, respectively) of the HRV during the whole recovery period. RESULTS: Greater LF (from the min 5 to 10) and HF (from the min 6 to 10) in the post-exercise period in the H(igh)PT compared to the (Low)PT group (P < 0.05) was observed. CONCLUSION: These results indicate that exercise training exerts beneficial effects on post-exercise cardiac autonomic control.