Sphenoethmoidal meningoencephalocele is a rare congenital meningocele with unclear clinical course. Its clinical symptoms are diverse, and this disease is widely observed across all ages. The prognosis of this disease depends on the severity of the central nervous system complications. We reported a case of sphenoethmoidal meningoencephalocele incidentally discovered in a 2-yr-old patient, with the subsequent appearance of diabetes insipidus at school age. An endocrinological evaluation performed when the patient was nine years old using the TRH/CRH/LH-RH load test showed a low response of gonadotropins and slightly hyper-response and normal response of ACTH and TSH, respectively. GH provocative tests indicated severe GH deficiency. Desmopressin and GH treatment efficiently improved his growth rate and quality of life. His pituitary function had presumably been normal from the neonatal period to infancy, but the dysfunction gradually progressed over the next few years along with his physical growth. The symptoms were suspected to be the product of the natural course of his hypothalamus or pituitary gland degeneration, or were otherwise due to gradual damage by chronic mechanical compression or extension. These findings underscore the importance of conducting careful systemic management in the long term, specifically with respect to the endocrinological evaluation of sphenoethmoidal meningoencephalocele.