Balloon-occluded retrograde transvenous obliteration (BRTO) is widely used to treat isolated gastric varices (IGVs) in Japan. However, BRTO is difficult to perform for IGVs with many small collateral veins, and no secondary treatment has been established. We herein report a rare case of IGVs refractory to BRTO successfully treated by shunt-occluded endoscopic injection sclerotherapy (SO-EIS), which is a combination therapy of major shunt occlusion by a balloon catheter and endoscopic injection sclerotherapy. Since SO-EIS can be performed regardless of the IGVs' anatomical configuration, it may be a promising alternative treatment for IGVs refractory to BRTO.