Brainstem encephalitis caused by Epstein-Barr virus (EBV) is rare in childhood. We describe a 14-month-old-boy who presented with limitation of eye movements with sixth cranial nerve palsy. Brainstem encephalitis caused by EBV was diagnosed, based on the neuroimaging and cerebrospinal fluid (CSF), serological examination for EBV infection. Brain magnetic resonance imaging (MRI) showed high signal intensity in T2 and low signal intensity in T1 in both pons and medulla. The result of EBV polymerase chain reaction (PCR) of the CSF was positive, and a serological test showed a convalescent phase of primary infection: positive for viral capsid antigen (VCA)-IgM, VCA-IgG and EBV nuclear antigen (EBNA)-IgG, negative for heterophil antibody. We suggest that EBV infection should be considered a differential diagnosis cause of pediatric brainstem encephalitis and emphasizes the need for immediate diagnosis and initiation of symptomatic and specific therapy.