Here we present the case of an 11-year-old female patient diagnosed with Caroli syndrome, who had refractory esophageal varices. The patient had a history of recurrent bleeding from esophageal varices, which was treated with endoscopic variceal ligation thrice over a period of 2 years. However, the bleeding was not controlled. When the patient finally visited the Emergency Department, the hemoglobin level was 4.4 g/dL. Transhepatic intrajugular portosystemic shunt was unsuccessful. Subsequently, the patient underwent percutaneous transhepatic variceal obliteration. Twenty hours after this procedure, the patient complained of aphasia, dizziness, headache, and general weakness. Six hours later, the patient became drowsy and unresponsive to painful stimuli. Lipiodol particles used to embolize the coronary and posterior gastric veins might have passed into the systemic arterial circulation, and they were found to be lodged in the brain, kidney, lung, and stomach. There was no abnormality of the portal vein on portal venography, and blood flow to the azygos vein through the paravertebral and hemiazygos systems was found to drain to the systemic circulation on coronary venography. Contrast echocardiography showed no pulmonary arteriovenous fistula. Symptoms improved with conservative management, and the esophageal varices were found to have improved on esophagogastroduodenoscopy.