A 74-year-old noncirrhotic woman presented with abdominal distension and pain in the right hypochondrium. Contrast-enhanced computed tomography (CT) demonstrated multiple large simple liver cysts occupying the right lobe of the liver, the largest of which was 19 cm in diameter. Gastric varices were enhanced in the fundus of the stomach. The patient underwent surgery to deroof the hepatic cysts with ablation using argon beam coagulation. Esophagogastroduodenoscopy (EGD) showed that the portal hypertensive gastropathy was ameliorated after the operation; however, the fundal varices were only slightly decreased. After the operation, we observed that the hepatic vein waveform gradually changed from a gently curved pattern to a normal triphasic pattern. We treated the fundal varices with balloon-occluded retrograde transvenous obliteration 3 months after the initial operation. We describe our successful treatment of this rare case and discuss the utility of hepatic vein waveform analysis in the study of portal hypertension.