Previous studies suggest an altered circadian regulation of arousal in children with attention-deficit hyperactivity disorder (ADHD) as measured by activity, circadian preference, and sleep-wake patterns. Although heart rate is an important measure to evaluate arousal profiles, to date it is unknown whether 24-h heart rate patterns differentiate between children with and without ADHD. In this study, 24-h heart rate data were collected in 30 non-medicated children with ADHD (aged 6–11) and 30 sex-, class-, and age-matched normal controls in their naturalistic home and school setting, during 5 days. Simultaneously, 24-h activity patterns were registered. Confounding effects of demographic variables (e.g., age, sex, BMI, pubertal stage) and comorbid internalizing and externalizing problems on heart rate levels were additionally assessed. Longitudinal analysis showed that heart rate levels were overall higher in the ADHD group (p < 0.01)—with the largest effects during afternoon and night—in a model controlling for age. Other factors did not significantly contribute to variations in heart rate levels. Compared to controls, children with ADHD showed higher activity levels during daytime (especially early afternoon), but not during nighttime (p < 0.05). Post hoc analyses showed that environmental effects might influence daytime variations. Findings suggest an autonomic imbalance in children with ADHD as compared to controls, with higher heart rate levels in the ADHD group. Nighttime tachycardia in this group could not be explained by nighttime activity levels or comorbid externalizing/internalizing problems. Further research on autonomic functioning in ADHD is recommended because of the major impact of higher resting heart rate on health outcomes.