Pituitary stalk interruption and ectopic neurohypophysis seen on magnetic resonance Imaging (MRI) are often associated with either isolated growth hormone (GH) deficiency or combined anterior pituitary hormone deficiency, but their pathogenesis is not clear and the clinical data regarding these anatomical defect is limited. We experienced a 23-year-old male with the absence of secondary sexual characteristics and this was accompanied with pituitary stalk dysgenesis and ectopic neurohypophysis. He received growth hormone for a year when he was 12 years old due to his short stature. Sella MRI showed no visible pituitary stalk with minimal high signal change, suggesting ectopic neurohypophysis. The combined pituitary stimulation test revealed blunted responses of growth hormone, follicle stimulating hormone and luteinizing hormone. For the hypogonadotropic hypogonadism, the patient was given testosterone intramuscularly and he gradually developed secondary sexual characteristics. We concluded that the hypogonadism and growth hormone deficiency in this patient was caused by hypopituitarism due to pituitary stalk dysgenesis and ecopic nuerohypophysis.