Background: As double-outlet right ventriclehas a wide pathophysiology spectrum, its comprehensive treatment strategy is determined based on relevant factors, such as the location and size of the ventricular septal defect, ventricular volume, and relationship of the great arteries. However, for borderline double-outlet right ventriclecases, it is occasionally difficult to decide the treatment strategy preoperatively. Recently, advances in 3D printing technology based on computed tomography have enabled the creation of 3D heart models of congenital heart disease that can precisely reproduce the anatomical structure of each patient even for complex anomalies. Herein, we describe a young patient in whom univentricular repair could be decided after confirming the 3D heart model and intracardiac structure under direct vision. Case presentation: We describe a 3-year-old girl who was diagnosed with double-outlet right ventricleand severe pulmonary valve stenosis at birth and who underwent a left modified Blalock–Taussig shunt at 2 years of age. Preoperative examination revealed a borderline condition for biventricular repair characterized by a small left ventricle volume and side-by-side relationship of the great artery. After a preoperative discussion using a 3D heart model, we concurred that an intraoperative assessment would be made as to whether biventricular repair was possible or not. After confirming the intracardiac structure under direct vision, we assessed that intraventricular rerouting was not possible owing to the high risk of subvalvular aortic stenosis as there was no tissue that could be incised between the right ventricular free wall and the primary interventricular foramen, as indicated in the 3D heart model. Thus, atrial septostomy and Glenn anastomosis were performed. Conclusions: We report a 3-year-old girl with a borderline double-outlet right ventriclein whom a univentricular repair strategy could be decided after confirming the 3D heart model and intracardiac structure under direct vision. A 3D-printed heart model can be useful in patients whose repair strategy is difficult to judge for the borderline double-outlet right ventricle.