© 2021 Japan Pediatric SocietyBackground: Premature ventricular contractions and supraventricular contractions are common rhythm disorders requiring comprehensive investigation in children. The aim of the study was to evaluate the heart rate variability (HRV) in premature ventricular contractions (PVCs) and supraventricular contractions (PSVCs) in children. Methods: The study compared the characteristics of HRV in 175 children with PVCs and 160 children with PSVCs who underwent 24-h Holter monitoring, with 101 healthy children. Results: Significant differences were found between standard deviation of all normal RR intervals (SDNN), standard deviation of average RR intervals in all 5 min segments of registration (SDANN), root mean square of the successive differences (rMSSD), and the proportion of NN50 divided by total number of NNs (pNN50) values of the patient and control groups. The PVCs group had a significantly lower high frequency (HF) and higher low frequency (LF)/HF ratio and the PSVCs group had a significantly higher LF and higher LF/HF ratio compared to the control group. No significant correlation existed between frequency and the SDNN index, rMSSD, and pNN50 values of the PVCs group. The receiver operating characteristics analysis showed a significantly changed LF/HF ratio when premature contractions exceeded 60 beats per hour in children with PVCs. Conclusions: This study indicated an increased sympathetic tone and a significantly decreased vagal tone in children with PVCs and PSVCs. HRV can be used increasingly as a non-invasive method in the follow-up of children with premature cardiac contractions.