Objective: There are conflicting reports in the literature concerning the time and frequency domain parameters of heart rate variability (HRV) in athletes. Furthermore, the exact impact of different sports disciplines on cardiac autonomic function is unclear. Thus, the study was destined to assess and compare HRV in the time and frequency domains between elite Nepalese football players and non-athletes. Methods: Temporal and spectral HRV parameters determined from 5-minute continuous ECG during supine rest were studied in 27 elite male football players (age: 22.74±2.52 years) with excellent cardiorespiratory fitness, and 30 non-athletic male (age: 23.41±2.95 years) volunteers (control group). All HRV parameters were compared between the groups. Results: Resting heart rate, systolic and diastolic blood pressure were significantly lower and all parasympathetic-related time and frequency domain indices, including root mean square of successive differences [RMSSD, [HFnu,)%, p=0.001]), were higher in footballers compared to non-athletics. Similarly, standard deviation of all NN intervals (SDNN), determinant of global HRV, was higher in players (p=0.003). Furthermore, the power spectral components low frequency in normalized unit (LFnu), a sympathetic marker, and LF/HF, which reflect sympatho-vagal balance, were significantly lower in players. Conclusion: The footballers had enhanced parasympathetic (higher RMSSD, HF and HFnu, and lower LF/HF ratio) and diminished sympathetic (lower LFnu) tone on heart. Football playing has favorable effect on the cardiac autonomic profile as indicated by high global HRV (higher SDNN).