Sphenoid sinus malignancies are rare diseases. Secondary hypopituitarism associated with sphenoid sinus malignancy is not well known. A 41-year-old male complained of right ptosis. Neurological findings revealed right oculomotor, trochlear and glossopharyngeal nerve palsy. Imaging diagnosis suggested a tumor that had spread bilaterally from the sphenoid sinus to the ethmoid sinus, nasopharynx and posterior pharyngeal space. Biopsy revealed squamous cell carcinoma (SCC). Based on these findings, a clinical diagnosis of SCC of the sphenoid sinus was made. Removal of the tumor without damaging nearby organs would have been difficult because the tumor extended to the bilateral optic nerves, optic chiasma and internal carotid artery, and surgeons, therefore, recommended proton beam therapy (PBT). Before PBT, the hypopituitarism occurred in the patient and we administered hydrocortisone and levothyroxine. During treating for hypopituitarism, we performed PBT with nedaplatin and 5-fluorouracil. The daily PBT fractions were 2.2 relative biological effectiveness (RBE) for the tumor received total dose of 81.4 Gy RBE. The acute side effect of grade 2 dermatitis according to the National Cancer Institute Common Terminology Criteria for Adverse Events version 4.0. Occurred after PBT. The patient needs to take hydrocortisone and levothyroxine, but he remains in complete remission 8 years after treatment without surgery or chemotherapy. Visual function is gradually declining, but there is no evidence of severe radiation-induced optic neuropathy.