In this report, we describe unilateral medial pontomedullary junction (MPMJ) syndrome as a novel brain stem stroke syndrome. A 68-year-old woman suddenly developed vertigo, ipsilateral facial paresis, contralateral thermal hypoalgesia (TH) and dysphagia without lateral gaze palsy, curtain sign and hoarseness. Magnetic resonance (MR) imaging showed a small infarction at the right MPMJ. MR angiography did not show vertebrobasilar arterial dissection, thrombosis or vasospasm. Finally, her dysphagia regressed over 4 weeks in synchronization with recovery of TH. To the best of our knowledge and based on a review of the literature, this MPMJ syndrome associated with the unilateral MPMJ infarction is a novel brain stem stroke syndrome different from Foville syndrome, Millard-Gubler syndrome, Wallenberg syndrome or Dejerine's syndrome. In the MPMJ syndrome, transient, albeit severe, dysphagia based on the TH-impaired swallowing reflex bothered the patient more than hemiparesthesia of TH did.