We report unusual cases of brainstem encephalitis in two young boys. Both presented with acute febrile illness, progressive encephalopathy, and marked cerebrospinal fluid pleocytosis. Case one shared some of the clinical features that have been seen in previously reported cases of brainstem encephalitis, such as ophthalmoplegia, ataxia, and progressive encephalopathy. Case two presented with similar clinical features, although without ophthalmoplegia and ataxia. A review of magnetic resonance imaging revealed mild differences with respect to anatomic lesion localization and confirmed a neuroanatomic basis for the variance in each patient’s symptoms. The features of these cases deviate from the classical symptoms described in the Miller-Fisher syndrome/Bickerstaff brainstem encephalitis/Guillain-Barré syndrome spectrum, although the cause for variability in clinical phenotypes is unknown.