Primary partial empty sella occurs when less than 50% of an enlarged or deformed sella turcica is filled with cerebrospinal fluid in the setting of unidentified etiologic pathological conditions. Prepubertal hypogonadotropic hypogonadism presenting as its main manifestation is rare since its peak incidence commonly occurs late at 30 to 40 years of age and has a sexual predilection for female. We described a case of 20-year-old male who presented with micropenis and absent secondary sex characteristics. Work up showed cranial MRI finding of partial empty sella, low testosterone, LH, FSH, Estradiol and Beta HCG levels. Sex hormone replacement may not improve fertility for this case but may help produce and maintain virilization and prevent future complications of hypogonadotropic hypogonadism.