Low baroreflex sensitivity (BRS) and heart rate variability (HRV) are associated with the pathogenesis of adult hypertension. However, limited information exists about the negative consequences of elevated childhood blood pressure (BP) and autonomic regulation. Additionally, there are developmental changes in autonomic regulation throughout puberty, yet studies have not appropriately accounted for this. The objective of this study was to investigate BRS and HRV in children with 2 different BP profiles, while controlling for the effects of maturation, age, sex, and body composition. A sample of 11- to 14-year-old participants were divided into 2 BP groups: high BP (HBP; ≥95th percentile; n = 21) and normal BP (NBP; <90th percentile; n = 85). Automated BP was measured at 2 time points. In lab-based testing, 5 min of beat-to-beat BP (Finapres) and R-R interval (RRI) were recorded (standard electrocardiogram) after 15 min of supine rest. Spectral indices were computed using fast Fourier transform, and transfer function analysis was used to compute BRS. High frequency (HF) and low frequency (LF) power spectral areas were set to 0.15-0.4 Hz and 0.04-0.15 Hz, respectively, and BRS was determined for the LF area. After adjustment for age, sex, maturation, and body composition, BRS (p = 0.04), LF (p = 0.008), and HF (p = 0.01) RRI variability, and RRI total power (p = 0.005) were lower in the HBP than in the NBP participants. As well, the LF/HF systolic BP variability ratio was higher in the HBP than in the NBP group (p = 0.03). Despite their young age, these children with high, yet not clinically hypertensive BP, display reduced autonomic regulation.