Wernicke's encephalopathy is caused by thiamine deficiency, and is characterized by acute mental confusion, ataxia, and ophthalmoplegia. It is also a rare neurologic complication of hematopoietic stem cell transplantation (HSCT). However, because of its rare incidence, Wernicke's encephalopathy can easily be overlooked in HSCT patients, and a few misleading steps in the early stage of the disease may result in permanent neurologic disability or even mortality. We recently encountered a case of Wernicke's encephalopathy in a patient who underwent allogeneic HSCT. Based on our own experience and previously published documents, we suggest early radiologic surveillance and treatment for patients with findings compatible with Wernicke's encephalopathy following HSCT.