We evaluated the effect of endoscopic sinus surgery on irradiation-induced rhinosinusitis of the maxillary-sinus mucosa among patients with nasopharyngeal carcinoma (NPC). Surgical outcomes were evaluated by changes to the ultrastructure of the antral mucosa and nasomucociliary clearance. Twenty-one NPC patients with irradiation-induced chronic sinusitis were enrolled in the study, along with five controls. Specimens were taken from 42 maxillary sinuses during surgery and 1 year after surgery. Saccharin transit time was measured before the initial surgery and 1 year after surgery. In the postoperative cases, we found a decrease in the number of the submucosal gland openings (P < 0.05), the cilia in the antral mucosa regenerated (P < 0.05), and the saccharin transit time reduced (P < 0.05); the number of goblet cells did not change. Endoscopic sinus surgery is an effective treatment for irradiation-induced rhinosinusitis in NPC patients, improving ventilation and drainage of the paranasal sinuses, and facilitating regeneration of the sinus mucosa.