Persistent idiopathic facial pain (PIFP), previously termed atypical facial pain, is a continuous facial pain that does not have the classic characteristics of cranial neuralgias and is not attributable to a different disorder. We report a case of PIFP which was misdiagnosed as temporomandibular disorder (TMD) by several doctors. A 47-year-old man was referred to our institution with a history of left persistent facial pain for six months. The quality of the pain was a continuous pulling or throbbing pain around the left temporomandibular joint. The pain had an intensity of 8 in a numerical rating scale from 0 to 10 and was not triggered or aggravated by jaw movement. Physical examination failed to show any intraoral or extraoral disease. An X-ray examination of the jaws and magnetic resonance imaging of the head and face as well as the temporomandibular joint did not demonstrate relevant abnormality. According to the International Classification of Headache Disorders-2 criteria, PIFP was diagnosed. The cause of the PIFP was not determined, but psychosocial factors interacted with the PIFP. Cognitive behavioral therapy relieved the PIFP. Within chronic orofacial pain, the diagnosis of PIFP is difficult as PIFP must be distinguished from other facial pains including TMD. The PIFP could be differentiated from TMD by pain that is persistent, spontaneous, and not triggered or aggravated by jaw movement or provocation test. Cognitive behavioral therapy may be considered for PIFP patients with cognitive distortions.