Citrin deficiency caused by SLC25A13 gene mutations develops into adult-onset type II citrullinemia (CTLN2) presenting with hepatic encephalopathy. Recent studies have suggested that excessive loading of carbohydrates is harmful in citrin-deficient individuals. Here we report a CTLN2 patient who showed further deterioration of encephalopathy after the employment of conventional low-protein diet therapy for chronic liver failure. Owing to the high carbohydrate content, the conventional low-protein diet therapy should be avoided in patients with hepatic encephalopathy associated with citrin deficiency. In addition, our observation may suggest that carbohydrate-restricted diet in which the content of carbohydrate is below 50% of daily energy intake can have therapeutic efficacy in CTLN2 patients.