Background The optimal surgical strategy for pulmonary atresia with ventricular septal defect (PA/VSD) in neonates and young infants is controversial. Staged repair may be associated with a higher risk of inter-stage mortality, while primary repair may lead to frequent post-repair re-interventions. Methods From 2004 to 2017, 65 patients with PA/VSD who underwent surgical intervention before 90 days of age were identified and enrolled in this retrospective study. The cohort was divided into two groups: group-SR, who underwent initial palliation with staged repair (n = 50), and group-PR who underwent primary repair (n = 15). Results There were three post-palliation in-hospital mortalities, four inter-stage mortalities, and one post-repair in-hospital mortality in group-SR. In group-PR, there was one in-hospital death and one late death. Five-year survival rates were comparable between the two groups (group-SR: 83.6%; group-PR: 86.7%; p = 0.754). During the median follow-up duration of 44.7 months (Inter-quartile range, 19-109 months), 40 post-repair re-interventions (22 in group-SR, 18 in group-PR) were performed in 26 patients (18 in group-SR, 8 in group-PR). On Cox proportional hazards model, primary repair was identified as the only risk factor for decreased time to death/1st post-repair re-intervention (Hazard ratio (HR): 2.3, p = 0.049) and death/2nd post-repair re-intervention (HR 2.91, p = 0.033). Conclusions A staged repair strategy, compared with primary repair, was associated with comparable overall survival with less frequent re-interventions after repair in young infants with PA/VSD. Lowering the inter-stage mortality after initial palliation by vigilant outpatient care and aggressive home monitoring may be the key to better surgical outcomes in this subset.