BACKGROUND: Wernicke encephalopathy is rare in children and is caused by thiamine deficiency. It is characterized by acute or subacute ataxia, altered consciousness, and ophthalmoparesis. Gastroenterological surgery, total parenteral nutrition for short bowel syndrome, and alcoholism are common risk factors for Wernicke encephalopathy. Typical magnetic resonance imaging features include selective symmetrical signal changes in the mammillary bodies, medial thalamus, tectum, periaqueductal region, cranial nerves, cerebellum, red nucleus, dentate nucleus, fornix, splenium, cerebral cortex, and putamen. If left undiagnosed and untreated, the disease may be fatal. PATIENT DESCRIPTION: We describe a 13-year-old boy who developed acute cerebellar findings while receiving total parenteral nutrition after gastroduodenostomy for duodenal stenosis. RESULTS: The diagnosis of Wernicke encephalopathy was based on his clinical history, neurological examination, and imaging results. We immediately started intravenous thiamine replacement therapy. Two weeks later, the patient's clinical signs had resolved except for mild clumsiness, which was observed during his tandem gait examination. CONCLUSION: Our report emphasizes the importance of clinical and magnetic resonance imaging pattern recognition in timely diagnosis, as well as the importance of prompt thiamine replacement therapy. We also demonstrate the importance of thiamine supplementation during total parenteral nutrition after gastrointestinal surgery.