Thiamine plays a critical role in energy metabolism. Critically ill children and adults may develop thiamine deficiency with ultimately increased mortality due to potentially irreversible consequences of severe type B lactic acidosis. We report a case of an unvaccinated term neonate with malignant pertussis requiring extracorporeal membrane oxygenation and continuous renal replacement therapy, who developed profound lactic acidosis of unknown etiology. After countless evaluations for likely causes, the patient was ultimately determined to have thiamine deficiency and her acidosis resolved rapidly with vitamin supplementation.