Heart rate variability (HRV) is a non-invasive quantitative marker of cardiac autonomic function derived from continuous electrocardiogram (ECG) recordings. Normative HRV values and development factors have not been established in pediatric populations. The objective was to derive referent time- and frequency-domain HRV values for a population-based sample of children. Children aged 9–11 years (N = 1,036) participated in the Québec Longitudinal Study of Child Development cohort cardiovascular health screening. Registered nurses measured anthropometrics (height, weight) and children wore an ambulatory Holter monitor to continuously record an ECG signal. HRV variables included time (SDNN, pNN50, RMSSD, SDANN) and frequency (HF, LF, LF/HF ratio) domain variables. Normative HRV values, stratified by age, sex, and heart rate, are presented. Greater heart rate (β _avg  = −0.60, R _avg ²  = 0.39), pubertal maturation (β _avg = −0.11, R _avg ²  = 0.01), later ECG recording times (β _avg = −0.19, R _avg ²  = 0.07), and higher diastolic blood pressure (β _avg = −0.11, R _avg ²  = 0.01) were significantly associated with reduced HRV in 10-year-old children. The normative HRV values permit clinicians to monitor, describe, and establish pediatric nosologies in primary care and research settings, which may improve treatment of diseases associated with HRV in children. By better understanding existing values, the practical applicability of HRV among clinicians will be enhanced. Lastly, developmental (e.g., puberty) and procedural (e.g., recording time) factors were identified that will improve recording procedures and interpretation of results.