Introduction Hypothalamic obesity (HO) is a type of obesity that is caused by hypothalamic damage. HO can be complicated by obstructive sleep apnea syndrome (OSAS) due to anatomical narrowing of the upper airway and hypothalamic damage-induced dysfunction of the sleep control mechanisms. We aimed to explore the presence and severity of OSAS in children with HO and hypothesized that OSAS is more severe and frequent in HO than exogenous obesity (EO). Methods This cross-sectional study was conducted among children aged 6.6-17.9 years. Subjects with HO (n = 14) and controls with EO (n = 19) were consecutively recruited through an endocrinology clinic. All patients underwent full-night polysomnography. The primary outcomes were obstructive apnea-hypopnea index (OAHI) and the severity of OSAS. We analyzed the polysomnography findings, biochemical parameters, Brodsky and modified Mallampati scores, and blood pressure compared with the controls. We explored the different obesity types and these variables in association with OAHI using multiple linear regression (MLR). Results Age and body mass indexzscores (BMI-z) were similar between the EO and HO groups. The OAHI of HO (5.8) was higher than that of EO (2.2). In MLR, the predicted OAHI was formulated as an equation using regression coefficients of obesity type (HO), age, and BMI-z(R-2 = .41). In the logistic regression analysis, the odds ratio of moderate/severe OSA was 5.6 for HO. Conclusions Children with HO have a higher risk of moderate/severe OSAS than children with EO. Polysomnography should be considered in all patients with HO.