The short gut syndrome can lead to multiple metabolic disorders along with chronic malnutrition. Such patients can develop changes in mental status due to metabolic alterations. We present a case of eleven years old male who presented to the hospital with an altered mental state. There were repeated admissions to the hospital with a similar complain with non-conclusive cerebrospinal fluid analysis and normal neuroimaging findings. The patient suffered from chronic malnutrition and multiple hospitalizations with altered mental status, encephalopathy. However, he responded well to bicarbonate therapy and prophylactic metronidazole treatment