A 40-year-old man presented with intractable headache of 5-year duration and a 1-month history of intermittent cerebrospinal fluid (CSF) rhinorrhea. Magnetic resonance imaging showed a cystic lesion with signal characteristics similar to that of CSF. The patient underwent endonasal endoscopic surgery of the sphenoid sinus and the fistula was reinforced with facia, muscle cartilage, and posterior septal flap while performing cystocisternostomy. The postoperative course was uneventfiul CSF leakage stopped, and headache improved. Postoperative imaging revealed total collapse of the cyst cavity. Based on our findings, endonasal endoscopic treatment of the sellar and parasellar arachnoid cysts, if presenting into the sphenoid sinus, could be an acceptable minimally invasive alternative to the conventional modalities.