Background – During rhythmic exercise, overall, heart rate variability (HRV) decreases with increasing intensity, and resting measurements do not reliably reflect responses during activity. Nonneural oscillations in the high-frequency band caused by increased respiratory effort further complicate HRV interpretation. Autonomic nervous system (ANS) balance, particularly between parasympathetic and sympathetic activity, is crucial for optimal athletic performance, highlighting the importance of non-invasive assessments. This study aimed to examine the acute effects of aerobic versus anaerobic running on HRV and ANS indices in male college athletes. Methods – We evaluated the effects of rest, aerobic running (AeR) and anaerobic running (AnR), recovery on HRV and ANS indices in 25 healthy male college athletes. Each athlete ran for a mean of 30.96 minutes at low intensity for aerobic running, and an average of 2.59 minutes at high intensity for anaerobic running. RR intervals were recorded using a Polar watch with H10 chest strap and analyzed with Kubios HRV Scientific software using time- and frequency-domain HRV measures, including low-frequency (LF, 0.045–0.15 Hz) and high-frequency (HF, 0.15–1.0 Hz) components. Results – Significant differences were found between AeR and AnR in terms of LF, HF, SNS index, and LF/HF ratio. Differences were also found in RMSSD, SD1, SD2, SNS index, and pNN50 values ​​after AeR and AnR (P<0.05). In within-subject comparisons, during AeR, RMSSD, SD2, pNN50, and PNS index decreased, but SD1 and SNS increased significantly (P<0.05). RMSSD and pNN50 showed no increase or decrease after AeR. SD1 and SNS index decreased after AeR on the other hand, PNS index increase (P<0.05). During AnR, RMSSD, SD2, pNN50, LF, LF/HF ratio decreased, but HF, SD1 and SNS index increased significantly (P<0.05). Compared to the resting state, SD1 and SD2 did not show any change after AnR, but LF, LF/HF ratio, SD1, and SNS index increased, while RMSSD, pNN50, HF, and PNS index decreased. Conclusion – It was found that the SNS was more dominant during both AeR and AnR. The SNS was more activated during AnR than during AeR. It was observed that college athletes were exposed to more psychophysiological stress during AnR. During the 10-minute post-run recovery period, PNS activation approaches pre-run levels, while SNS activation tends to be higher. The body needs more than 10 minutes to recover after an AnR.