A 68-year-old female with autosomal dominant polycystic kidney disease (ADPKD) on hemodialysis underwent transcatheter arterial embolization (TAE) of the renal arteries with complaints of dyspnea and gastrointestinal symptoms due to enlarged kidneys. One month after renal TAE, consciousness disturbance associated with hyperammonemia occurred. Abdominal angiography demonstrated a spleno-renal shunt and was suspected to the cause of portal-systemic encephalopathy. Since hyperammonemia was resistant to lactulose and branched chain amino acid, the shunt-preserving disconnection of portal and systemic circulation using an interventional radiology method was selected. After successfully performing this procedure, consciousness disturbance improved. It is suggerted that the blood flow of the hepatic and portal vein were obstructed by the massive hepatic cysts, and it goes into the extra portal vein including the splenic vein, resulting in a spleno-renal shunt. The preexisting spleno-renal shunt became symptomatic due to changes in hemodynamics after renal TAE. The renal TAE therapy in ADPKD patients was started in 1996 and has been reported to be a safe and effective therapy. However, there is a possibility of both portal-systemic shunt and portal hypertension in patients with ADPKD. This is the first case of ADPKD patient who developed portal-systemic shunt encephalopathy after this procedure.