Extrahepatic portal-systemic shunts cause portal-systemic encephalopathy. Direct communication between the inferior mesenteric vein (IMV) and the inferior vena cava (IVC) is a relatively rare pathway among the variety of portal-systemic shunts. This report describes a case of successful occlusion of an IMV-IVC shunt. Based on laboratory data and computed tomography findings, a 69-year-old woman with liver cirrhosis was diagnosed with portal-systemic encephalopathy due to a shunt between the IMV and the IVC. Her hepatic coma had not been adequately controlled by oral or intravenous pharmacotherapy. First, we placed a covered stent in the main trunk of the portal vein and the superior mesenteric vein (SMV) to block the SMV hepatofugal flow and splenic vein hepatopetal flow, but this therapy showed only a transient therapeutic effect due to recanalization. Next, we performed balloon-occluded retrograde transvenous obliteration (BRTO) of the portal-systemic shunt. After the BRTO, she has had no episodes of portal-systemic encephalopathy for 2 years.