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A couple of cysts lying in the pterygopalatine fossa are rare. The authors report a case of a 28-year-old woman who was admitted to the authors’ hospital with a 1-month history of headache and numbness on the left head. Three-dimensional computed tomography revealed a large soft mass in the pterygopalatine fossa. Magnetic resonance imaging showed that there were a couple of cysts in the pterygopalatine fossa. One cyst measured 41 × 38 × 34 mm and the other 23 × 19 × 19 mm. A transpterygoid transnasal endoscopic approach and resection of the lesion was performed. The authors opened the cyst with coblation and the lesion showed a lot of transparent thick yellow liquid. The authors located the posterior wall the other cyst with ENT image navigation. The puncture was conducted and a lot of yellow liquid flowed out of the lesion. The patient recovered rapidly. The headache and numbness were alleviated and disappeared after 1 month. The patient currently has no evidence of recurrence at 1 year postoperatively. The coblation and ENT image navigation make the surgeon more easily to achieve risk-free surgery under endoscopy.