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Nasopalatine duct cysts are the most common non-odontogenic cysts in the maxilla, and are conventionally treated through a sublabial or palatine approach. Recently, the endoscopic approach has been used, but experience is extremely limited. We treated a 29-year-old male with nasopalatine duct cyst by endoscopic marsupialization, but paresthesia of the incisor region occurred after surgery. This paresthesia gradually remitted within 6 months. The nasopalatine nerve, which innervates the upper incisor region, enters two lateral canals separately at the nasal floor and exits the central main canal at the palate. Damage to the bilateral nasopalatine nerves might lead to paresthesia, so we recommend careful examination for nerve fibers during endoscopic surgery, especially if fenestration is performed on both sides.