Objective: Dysregulation of the autonomic nervous system is thought to be involved in craniopharyngioma-related hypothalamic obesity (CRHO). Increased parasympathetic activity and decreased sympathetic activity have been suggested. We aimed to study autonomic activity using heart rate variability (HRV) and biochemical measures in youth with CRHO compared with controls and to explore relationships between obesity and autonomic indices. Design: A cross-sectional study of 16 youth with CRHO and 16 controls matched for sex, age, and BMI. Methods: Anthropometrics, fasting blood-work, resting energy expenditure (REE), 24-h HRV, and 24-h urine catecholamines were assessed. Quality of life, sleepiness, and autonomic symptoms were evaluated. Power spectral analysis of the HRV was performed. Results: HRV power spectral analysis parameters of both parasympathetic activity (mean high frequency (HF (ms 2 )) 611G504 vs 459G336, PZ0.325) and sympathetic activity (median low frequency/HF 1.62 (1.37, 2.41) vs 1.89 (1.44, 2.99), PZ0.650) did not differ between the groups. Parasympathetic activity negatively correlated with central adiposity in both groups (rZK0.53, PZ0.034 and rZK0.54, PZ0.029) and sympathetic activity positively correlated with central adiposity in CRHO (rZ0.51, PZ0.043). Youth with CRHO had significantly lower REE; lower health and activity scores in the quality of life questionnaires, and higher sleepiness scores. Conclusions: Autonomic activity was similar in CRHO and control subjects. The degree of central adiposity correlated negatively with parasympathetic activity and positively with sympathetic activity in children with CRHO. These results provide a new perspective regarding autonomic balance in this unique patient population.