Brainstem encephalitis may be a serious complication of enteroviral infection. Mainly due to human enterovirus A71, it has become a real health issue in Asia Oceania. In Europe, infection remains sporadic or causes small epidemics. Here we report an original case of Coxsackie B3 brainstem encephalitis, the first one to the best of our knowledge. A healthy five years old girl developed brainstem involvement signs. Clinical examination showed no fever, normal heart frequency and normal blood pressure. She presented a self-limited divergent squint which lasted 2 hours followed by oculomotor troubles and a right facial palsy. Biological tests performed on cerebrospinal fluid were not informative. The cerebral Magnetic Resonance Imaging was compatible with a rhombencephalitis. She totally recovered one month after this episode.Enterovirus was detected by real-time PCR on the nasopharyngeal and the stool sample collected on day of admission but was not detected on the cerebrospinal fluid. Coxsackie B3 was genotyped by sequencing of VP1 protein coding sequence. Despite the absence of enterovirus detection on the cerebrospinal fluid, the diagnosis of enterovirus rhombencephalitis was classified as probable by the French National Reference Centre for enterovirus. Our description highlights the necessity of nasopharyngeal and stool sampling in order to extend the diagnosis with the aim of learning about enterovirus circulation in Europe as well.