Septo-Optic Dysplasia (SOD) is a heterogeneous condition defined by any combination of i) optic nerve hypoplasia, ii) hypopituitarism, and iii) midline brain anomalies such as agenesis of the corpus callosum and absence of the septum pellucidum. We encountered a Japanese girl with optic nerve hypoplasia, growth failure, precocious puberty, and mild developmental delay. Her optic nerve hypoplasia was diagnosed at 4 months of age. Thereafter, she showed growth failure from infancy. Gradual breast development was noticed from 6 years of age. Therefore, she was referred to us at 9.2 years of age. Endocrinological investigations demonstrated deficiencies in growth hormone, adrenocorticotropic hormone, and cortisol. However, serum levels of luteinizing hormone, follicle stimulating hormone, and estradiol were increased to pubertal levels. Brain MRI revealed bilateral optic nerve hypoplasia, a normal anterior pituitary lobe, an invisible pituitary stalk, and an invisible posterior lobe. Based on these findings, she was diagnosed as having SOD with growth hormone deficiency, secondary adrenal insufficiency, and central precocious puberty. Replacement of hydrocortisone, recombinant growth hormone replacement, and suppression therapy by gonadotropin releasing hormone analog were initiated. Her growth rate and physical activity were improved after treatment. While SOD is rare, children with optic nerve hypoplasia should be carefully checked for symptoms of pituitary hormone deficiency. Timely diagnosis of endocrine deficits could reduce the morbidity of patients with SOD.