Chronic nasopharyngeal mucositis should be diagnosed and treated after nasopharyngeal neoplasm, autoimmune, post-radiotherapy, post-chemotherapy mucositis or gastroesophageal reflux was ruled out. A 52-year-old male presented with nasopharyngeal pain, blood-tingled sputum and left nasal stuffiness for 7.5 years. Septal deviation to left side, and injection, ulceration, and mild oozing of nasopharynx were identified. Nasopharyngeal biopsy revealed chronic inflammation, and other blood examinations reported normal. Upper digestive scopy revealed normal. However, all conservative treatment failed to cure off his disease. Unexpectedly, one month after septoplasty, the disease was cured. Then the postoperative course was uneventful in the following two years.