Persistent Idiopathic Facial Pain (PIFP) is a poorly understood chronic pain syndrome of the face, formerly known as atypical facial pain. It is characterized by a constant painful sensation without neurological abnormalities and without clinically objectifiable cause. Similarities to neuropathic pain conditions have been discussed and are currently thought to be relevant for the pathophysiology of this disease. In this study we aim to characterize the trigeminal pain processing in PIFP via functional magnetic resonance imaging (fMRI) of the brainstem.25 patients suffering from PIFP and 25 healthy controls (HC) underwent a standardized and well-established paradigm of painful stimulation of the trigeminal nerve using gaseous ammonia. Functional images were acquired within a 3T MRI scanner using an optimized protocol for high resolution echoplanar brainstem imaging.PIFP patients show exclusively a stronger activation to painful stimulation in the spinal trigeminal nucleus (sTN) when contrasted against HC.Our data suggest that abnormal central pain processing plays a role in the pathophysiology of PIFP. An integration of these findings into neuropathic pain models might help to gain a better general understanding of the pathophysiology of PIFP.