A 74-year-old man with compensated hepatitis C virus-related liver cirrhosis was admitted for the treatment of small hepatocellular carcinoma (HCC) by radiofrequency ablation therapy (RFA). As a routine pretreatment examination, gastrointestinal endoscopy was performed, and large nodular varices were observed in the gastric fornix, with telangiectasia on top of the varices. As soon as the RFA was completed, prophylactic balloon-occluded retrograde transvenous obliteration (B-RTO) was performed. Seven days after the B-RTO, the patient complicated of upper abdominal pain. Gastrointestinal endoscopy was performed, and a deep ulcer, located at the top of the tumor-shaped gastric varices, was found. The ulcer showed rapid healing after 1-week administration of a proton pump inhibitor (PPI). A severe ulcer after a B-RTO procedure, is extremely rare, because sclerosing agents rarely flow into the gastric mucosa. The ulcer in this patient was deep and large, and it may have been due to direct mucosal damage caused by the sclerosing agent, because mucosal telangiectasia on top of the varices was observed before the B-RTO. It is likely that, in this patient, the mucosal vessels communicated with the submucosal large varices, and ethanolamine oleate (EOI) flowed into the gastric mucosa via this communication. Based on our experience, we recommend periodic follow-up endoscopy.