A 3-year-old boy with portosystemic shunt developed refractory minimal hepatic encephalopathy that did not respond to lactulose, rifaximin, dietary changes, or probiotics. Treatment with glycerol phenylbutyrate significantly reduced median serum ammonia levels from 64.0 µmol/L to 55.0 µmol/L (P = 0.0268) and led to sustained behavioral and cognitive improvement with no hepatic encephalopathy events over 24 months. This case suggests glycerol phenylbutyrate may be an effective secondary ammonia scavenge therapy for noncirrhotic patients with portosystemic shunts and refractory hyperammonemia.