Congenital hypopituitarism is a possible cause of neonatal cholestasis, but the mechanism is still unknown. The pathogenesis of cholestasis may be due to hormone deficiency, which has effects on the physiological maturation of bile acid synthesis and transport. We experienced a case presenting with cholestasis and recurrent hypoglycemia associated with congenital hypopituitarism. Cholestasis resolved with thyroxine and hydrocortisone replacement therapy.