Purpose The purpose of this study was to compare heart rate (HR) and heart rate variability in young endurance athletes during nocturnal sleep and in the morning; and to assess whether changes in these values are associated with changes in submaximal running (SRT) and counter-movement jump (CMJ) performance. Methods During a three-week period of similar training, eleven athletes (16 ± 1 years) determined daily HR and heart rate variability (RMSSD) during sleep utilizing a ballistocardiographic device (Emfit QS), as well as in the morning with a HR monitor (Polar V800). Aerobic fitness and power production were assessed employing SRT and CMJ test. Results Comparison of the average values for week 1 and week 3 revealed no significant differences with respect to nocturnal RMSSD (6.8%, P = 0.344), morning RMSSD (13.4%, P = 0.151), morning HR (-3.9 bpm, P = 0.063), SRT HR (-0.7 bpm, P = 0.447), SRT blood lactate (4.9%, P = 0.781), CMJ (-4.2%, P = 0.122) or training volume (16%, P = 0.499). There was a strong correlation between morning and nocturnal HRs during week 1 (r = 0.800, P = 0.003) and week 3 (r = 0.815, P = 0.002), as well as between morning and nocturnal RMSSD values (for week 1, r = 0.895, P<0.001 and week 3, r = 0.878, P = 0.001). Conclusion This study concluded that HR and RMSSD obtained during nocturnal sleep and in the morning did not differ significantly. In addition, weekly changes in training and performance were small indicating that fitness was similar throughout the 3-week period of observation. Consequently, daily measurement of HR indices during nocturnal sleep provide a potential tool for long-term monitoring of young endurance athletes.