This study retrospectively evaluated long-term post-operative aortic and pulmonary valve functions in outlet ventricular septal defects. We evaluated aortic regurgitation and pulmonary regurgitation using pre- and post-operative echocardiograms. Overall, 158 patients who underwent intracardiac repair due to outlet ventricular septal defects with aortic valve deformity or congestive heart failure were included. The median follow-up period was 7years (interquartile range: 0-17years), without deaths or pacemaker implantations. The age, weight, ventricular septal defect size, and mild aortic regurgitation at surgery were factors associated with post-operative residual aortic regurgitation. Mild pulmonary regurgitation was observed in 12%, 30%, and 40% of patients 5, 10, and 15years after surgery, respectively. There were no significant differences in age and weight at which surgery was performed between patients with mild pulmonary regurgitation and those with less than mild pulmonary regurgitation. However, the number of sutures across the pulmonary valve was associated with post-operative pulmonary regurgitation (P < 0.01). As some patients with mild pre-operative aortic regurgitation may not improve even after surgery, early surgical intervention is necessary when aortic regurgitation appears. Some patients may develop post-operative pulmonary regurgitation in the long term, suggesting the need for careful follow-up.