Background: Aerobic exercise and relaxing music induce parasympathetic activity over the heart. The combined effect of the two interventions was shown to reduce heart rate (HR), rate of perceived exertion (RPE), and anxiety levels. Objectives: The purpose of the study was to evaluate the effect of aerobic exercise along with music vs. only aerobic exercise, on the autonomic function of the heart during recovery in collegiate overweight and obese individuals. Methods: Thirty-two collegiate overweight and obese individuals were recruited based on inclusion and exclusion criteria. Random allocation of participants was done to the aerobic exercise group (n = 16) and aerobic exercise plus music group (n = 16). Each group performed 30 minutes/session, six times/week for four weeks. Pre and post measures of body composition, exercise HR, RPE, square root of mean squared difference between adjacent R-R intervals (RMSSD), interval differences between of adjacent R-R intervals > 50 ms derived from difference between consecutive RR intervals (NN50), low-frequency (LF), high frequency (HF), and LF/HF measures of heart rate variability (HRV) during recovery were recorded. Results: RMSSD (P = 0.003) and LF (P = 0.009) scores showed a significant difference at baseline. A significant time effect was found to be in HR (P < 0.001), RPE (< 0.001), NN50 (P = 0.001), HF (P = 0.016) and LF/HF score (P < 0.001) of HRV indicating difference between pre and post measures, while no difference was found in RMSSD and LF score. A significant group effect was found to be in HR (P = 0.016) and LF/HF score (P = 0.008), indicating the difference between the two groups. Conclusions: Regular aerobic exercise, in conjunction with relaxing music, appears to confer a beneficial effect on the autonomic modulation during the post-exercise recovery period.