Spectral analysis of heart rate variability (HRV) has been widely used to investigate activity of autonomous nervous system. Previous studies demonstrated potential of analysis of short-term sequences of heart rate data in a time domain for continuous monitoring of levels of physiological stress however the value of HRV parameters in frequency domain for monitoring cycling exercise has not been established. The goal of this study was to assess whether HRV parameters in frequency domain differ depending on a stage of cycling exercise. We compared major HRV parameters in high, low and very low frequency ranges during rest, height of exercise, and recovery during cycling exercise. Our results indicated responsiveness of frequency-domain indices to different phases of cycling exercise program and their potential in monitoring autonomic balance and stress levels as a part of a tailored home-based telerehabilitation program.