Hyperammonemic encephalopathy is rarely caused by a urinary diversion. We herein experienced a case of rectal carcinoma with rectovesical and ileal fistulae that developed hyperammonemic encephalopathy. A 72-year-old man suffered from a fever, diarrhea, pneumaturia, and fecaluria beginning in April 2013 and was referred to our hospital in May 2013. He developed a loss of consciousness and whole body cramping on the first hospital day. The laboratory data indicated an inflammatory reaction and hyperammonemia with a highly elevated serum ammonia (NH3) level of 703 μg/dl.The patient was diagnosed to have rectal carcinoma with rectovesical and ileal fistulae according to computed tomography (CT) and a water-soluble contrast enema.We administered a solution of branched chain amino acids (BCAA) and antibiotics. Furthermore, we repeatedly irrigated bladder through the urethral catheter. The patient’s symptoms recovered, and the serum ammonia levels on the second and third hospital day were decreased to 210 and 135 μg/dl, respectively. However, the symptoms of infection and confusion were suspected to repeat; we elected to perform surgical treatment. An ileal disconnection with ileocecal bypass and sigmoidostomy were effective for preventing hyperammonemic encephalopathy.