A woman in her 50s was referred to our department with the chief complaint of nasal congestion and pharyngeal discomfort. The patient had been diagnosed with sleep apnea at the Department of Internal Medicine, and had undergone nasal continuous positive airway pressure (nCPAP) therapy, but her response to the treatment was poor. A cystic lesion occupying the nasopharynx, which was detected by nasopharyngeal fiberscopy, computed tomography, and magnetic resonance imaging, was thought to be the cause of the nasal congestion, pharyngeal discomfort, and obstructive sleep apnea syndrome (OSAS). Consequently, the patient underwent extirpation of the lesion under general anesthesia for the purpose of obtaining a definitive diagnosis as well as for treatment of the nasopharyngeal tumor. The diagnosis of intra-adenoid cyst was eventually made based on the pathological findings, which revealed lymphoid tissue accompanied by expansion of the crypt, as well as inflammatory cell infiltration with follicular hyperplasia. After the operation, the patient reported subjective improvement of her symptoms, and began to respond to the nCPAP therapy for her sleep apnea syndrome. Nasopharyngeal cysts, in particular adult intra-adenoid cyst, are relatively rare. The outcomes of the current case indicated that the presence of a nasopharyngeal cystic disease was hampering the nCPAP treatment of refractory OSAS.