Warthin’s tumors of the head and neck are more common in the parotid and salivary glands and are extremely rare in the nasopharynx. This paper reports the clinical data of a patient with a nasopharyngeal Warthin’s tumor and posterior nostril atresia who underwent nasal endoscopic nasal mass resection combined with posterior nostriphoplasty, and the patient has no tumor recurrence during the postoperative follow-up of until 14 months. This case report, combined with a literature review, conducted an in-depth analysis of nasopharyngeal Warthin’s tumors to enable more otolaryngology specialists to deepen their understanding of such diseases.