Attention-deficit/hyperactivity disorder (ADHD) has typically been diagnosed based on behavioral observations, symptom screening, and neuropsychological evaluations. Because of the lack of objective biomarkers of ADHD, ADHD may be overdiagnosed, leading to issues of drug abuse. Children with ADHD exhibit abnormalities in heart rate variability (HRV), which indicates cardiac vagal dysregulation and autonomic imbalances. However, a large database is required to ascertain whether these differences are observed in all children with ADHD. Therefore, this study investigated which HRV parameters were different between children with ADHD and neurotypical children. The results indicate that heart rate and age were indeed major factors that affect HRV. After controlling for age and heart rate, although the children with ADHD did not demonstrate differences in their time-domain parameters from the neurotypical children, among the frequency-domain parameters, they demonstrated higher nLF and LF/HF and lower nHF scores.