Management of isolated gastric varices with a gastropericardiac shunt (GPS) has not yet been established. We were able to control a case of isolated gastric varices with a GPS by percutaneous transhepatic obliteration (PTO) using a microcatheter. In this case, the main blood drainage route was not a gastrorenal shunt, so transvenous retrograde obliteration could not be performed and PTO using the microcatheter was applied. Percutaneous transhepatic splenic venography revealed that the gastric varices came from the posterior gastric vein and the main drainage route was a GPS. Gastric varices and their blood supply were superselectively embolized using platinum microcoils and absolute ethanol. Portal venous pressure did not change after PTO because the route from the left gastric vein to the azygos venous system was preserved. Computed tomography 7 days after PTO revealed that the gastric varices were completely obliterated by the thrombi. Plasma ammonia level, arterial ketone body ratio, and indocyanine green retention rate at 15 min were improved. We conclude that PTO using a microcatheter is a rational, effective, and safe therapy for isolated gastric varices with a GPS.