Background: This study aimed to compare the long-term outcomes of a modified réparation à l’étage ventriculaire (REV) and the Rastelli repair for ventricular septal defect (VSD) and pulmonary outflow tract obstruction without ventriculoarterial concordance. Methods: The study included 100 consecutive patients who underwent a modified REV (n = 50) or Rastelli repair (n = 50) for transposition of the great arteries, double outlet right ventricle, or double outlet left ventricle with VSD and pulmonary outflow tract obstruction. The mean ages of the patients who underwent the modified REV and Rastelli repair were 2.50 years (range: 0.30-12.48) and 5.91 years (range: 0.36-46.15), respectively (P < .05). Results: Actuarial survival and arrhythmia-free survival rates were 83.4% ± 4.0% (P > .05) and 72.4% ± 5.0%, respectively at 37.25 years (P > .05). The reoperation-free survival was 18.7% ± 4.6% at 31.82 years (P < .05). The freedom from the first, second, third, and fourth reoperations after the modified REV versus the Rastelli repair was 35.9% ± 8.3% at 29.8 years versus 6.7% ± 4.3% at 31.8 years (P < .05); 83.2%±6.3% at 29.8 years versus 21.2% ± 15.6% at 35.8 years (P < .05); 94.1% ± 4.1% at 29.8 years versus 56.1% ± 10.9% at 37.3 years (P < .05); and 97.0% ± 3.0% at 29.8 years versus 74.3% ± 10.2% at 37.3 years (P < .05), respectively. The most common causes of reoperation after the Rastelli repair were pulmonary stenosis, left ventricular outflow tract obstruction, and arrhythmia. However, the most common cause of reoperation after the modified REV was pulmonary regurgitation. Conclusion: Modified REV and Rastelli repair have shown satisfactory results in long-term follow-up. However, the Rastelli repair could not avoid repeated reoperations, especially for biventricular outflow tract obstruction and arrhythmia.