Primary solitary sphenoid sinus mucocele is rare, generally presenting with headaches or eye symptoms at the anatomical site. We report the case of a 39-year-old woman incidentally diagnosed with sphenoid sinus mucocele during a complete medical checkup. Imaging revealed that the cystic wall had developed from the rear sphenoid sinus and had spread expansively to diminish the clivus; however, no symptoms were reported, and the patient was managed with close observation. During the follow-up period, diplopia developed suddenly due to isolated left-sided abducens nerve paralysis. An endoscopic endonasal approach was used to open the frontal cystic wall, and fascia lata and fat were used for cranial base reinforcement to avoid future cerebrospinal fluid leakage, resulting in improvement during the early stages of follow-up. Treatment options for sphenoid sinus mucoceles include close observation or surgery. In our case, we chose surgery because of an acute symptomatic manifestation during observation.