Introduction: The purpose of this study was to investigate the effect of incremental running intensity on heart rate variability during recovery in university-level male football athletes. Methods: Twenty healthy males aged between 19-26 years old were randomly assigned to control (no running) and intervention (modified Bruce protocol running) groups. Analyses were performed at pre-exercise, 24, 48, and 72 h post-exercise. The low-frequency (LF) and high frequency (HF) in peak, absolute power and normalised unit (n.u.), as well as LF/HF ratio, were assessed. Results: Intervention group showed a reduced LF n.u. response (ES=1.69) whereas HF n.u. showed the opposite response (ES=1.51) at 24 h post-exercise. The intervention group showed a significant difference in the LF/HF ratio at 48 h post-exercise (p=0.002; ES=1.05). Conclusion: These findings demonstrated that incremental type of exercise influence both sympathetic and parasympathetic response for at least 48 h post-exercise.