Adult-onset periodic fever, aphthous stomatitis, pharyngitis, and cervical adenitis (PFAPA) syndrome is a rare condition, having been reported in only three patients in Japan till date. While almost all pediatric PFAPA patients respond well to tonsillectomy, some European studies have reported that tonsillectomy may be ineffective for adult-onset PFAPA. All the Japanese patients with adult-onset PFAPA had been treated orally so far (cimetidine with or without prednisone), instead of tonsillectomy. We reported a case involving a 37-year-old Japanese man with PFAPA syndrome who presented with a history of febrile episodes associated with pharyngitis, cervical adenitis, and aphthous stomatitis for one year. The patient had been undergoing oral medication therapy without any significant improvement. Tonsillectomy was performed for the patient, and complete resolution of PFAPA was achieved. Our experience suggests that a tonsillectomy is a viable option for the treatment of adult-onset PFAPA.