Thiamine (vitamin B) is a water-soluble vitamin that is not endogenously synthesized in humans. It is absorbed by the small intestine, where it is activated. Its active form acts as a coenzyme in many energy pathways. We report a rare case of thiamine deficiency in a 3.5-year old boy with short bowel syndrome secondary to extensive bowel resection due to necrotizing enterocolitis during his neonatal age. The patient was parenteral nutrition-dependent since birth and had suffered from recurrent central catheter-related bloodstream infections. He developed confusion with disorientation and unsteady gait as well as profound strabismus due to bilateral paresis of the abductor muscle. Based on these and a very low thiamine level he was diagnosed and treated for Wernicke encephalopathy due to incomplete thiamine acquisition despite adequate administration. He fully recovered after thiamine administration. After 1999 eight more cases have been reported in the PubMed mostly of iatrogenic origin.