We report a case of apical fenestration misdiagnosed as persistent apical periodontitis. The patient was a 55-year-old woman who presented with persistent tooth pain at the right maxillary canine, despite repeated root canal treatment by a general practitioner. When the patient visited Tokyo Dental College Suidobashi Hospital, a CT examination was performed and apical fenestration diagnosed. The patient received an apicoectomy after which the symptoms disappeared. This suggests that dentists should consider the possibility of apical fenestration when examining patients with persistent tooth pain after repeated root canal treatment.