Background When treating recalcitrant and severe childhood obesity, pharmaceutical options are limited and few patients qualify for bariatric surgery. A prolonged inpatient program serves as an alternative treatment. The purpose of this project was to describe the development of a medically supervised inpatient weight management program and evaluate its effectiveness. Methods This is a retrospective chart review of 18 patients [4-18 years, mean body mass index (BMI) 50.2 kg/m2] admitted to an inpatient pediatric weight management program from October 2011 through December 31, 2012 to evaluate the biometric, laboratory, sleep and behavioral changes that occurred from admission to discharge from the program. Results Average weight loss was 15% (6.9%-21.5%, p = 0.0001), the decrease in BMI was 15.1% (1.61-21.57, p = 0.0001), systolic blood pressure and diastolic blood pressure decreased by 7.2% (p = 0.003) and 10.3% (p = 0.040), respectively. The reduction in heart rate was 15% (p = 0.013). Upon admission, nine patients had obstructive sleep apnea syndrome (OSAS), of which one was treated with tonsillectomy and six were not compliant with home positive airway pressure (PAP) therapy. At discharge, three patients no longer required PAP and five required decreased PAP settings. Upon admission, seven patients met the criteria for an internalizing disorder. At discharge, symptom reduction was noted. Conclusion An intensive pediatric inpatient weight management program leads to successful weight loss, improvement in hemodynamic parameters, reduction in OSA treatment requirements and symptom improvement in anxiety and depressive disorders in obese children.