Bickerstaff's brainstem encephalitis (BBE) is a rare disease diagnosed by specific clinical features such as 'progressive, relatively symmetric external ophthalmoplegia and ataxia by 4 weeks' and 'disturbance of consciousness or hyperreflexia' after the exclusion of other diseases involving the brain stem. Anti-ganglioside antibodies (GM, GD and GQ) in the serum or cerebrospinal fluid (CSF) are sometimes informative for the diagnosis of BBE because of the rarity of positive findings in other diagnositic methods: brain magnetic resonance imaging (MRI), routine CSF examination, motor nerve conduction study, and needle electromyography. We report a rare case of childhood BBE with elevated anti-GM1 antibodies in the serum, who had specific clinical symptoms such as a cranial polyneuropathy presenting as ophthalmoplegia, dysarthria, dysphagia, and facial weakness; progressive motor weakness; altered mental status; and ataxia. However, the brain MRI, routine CSF examination, nerve conduction studies, electromyography, somatosensory evoked potentials, and brainstem auditory evoked potentials were normal. BBE was suspected and the patient was successfully treated with intravenous immunoglobulins.