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Heart rate variability (HRV) is an accepted method for determining autonomic nervous system activity and cardiovascular risk in various populations. This study assessed the validity and reliability of a commercially available finger photoplethysmography (PPG) system for measuring pediatric HRV in a real-world setting. Sixteen healthy children (4.06 ± 0.58 years) were recruited. The PPG system was compared to the Polar H10 heart rate (HR) sensor validated against ECG (gold standard) for HRV measurement. Seated short-term resting R-R intervals were recorded simultaneously using both systems. Recordings were performed on 3 days at the participants’ school. Paired t-tests, effect sizes and Bland–Altman analyses determined the validity of the PPG system. The relative and absolute reliability of both systems were calculated. No HRV parameters were valid for the PPG system. Polar H10 yielded moderate (0.50–0.75) to good (0.75–0.90) relative reliability with R-R intervals and the standard deviation of instantaneous and continuous R-R variability ratio showing the best results (ICCs = 0.84). Polar H10 displayed better absolute reliability with the root mean square of successive differences, R-R intervals and HR showing the lowest values (TEM% &lt, 12%). The use of the Polar H10 and not the PPG system is encouraged for HRV measurement of young children in an educational real-world setting.