Background <p>Management of pulmonary atresia with ventricular septal defect and ductal-dependent pulmonary circulation (PA/VSD/PDA) varies according to pulmonary artery morphology and institutional surgical strategy. We adopted a range of initial palliative surgical options for patients with PA/VSD/PDA and evaluated the effectiveness of our management strategy.</p> Methods <p>Twenty-five patients with PA/VSD/PDA were enrolled between May 2015 and July 2023. Patients with major aortopulmonary collateral arteries were excluded. The mean age at initial surgery was 14.9 ± 13.7 days, and the mean weight was 3.17 ± 0.35&#xa0;kg. Twenty-two (88%) patients were neonates. Nineteen patients underwent initial palliative systemic-to-pulmonary shunt, while six underwent an initial definitive Rastelli operation depending on the main pulmonary artery morphology and branch pulmonary arteries size.</p> Results <p>One patient died of postoperative brain hemorrhage following the initial definitive Rastelli operation. The mean follow-up duration was 58.5 ± 28.4 months. During follow-up, one patient died suddenly two months after the initial central shunt procedure. All surviving patients with a shunt, except two, underwent biventricular repair: ten with the Rastelli operation and six with the transannular patch (TAP) procedure. The staged TAP group demonstrated a significantly larger freedom from reoperation rate than that of the initial Rastelli operation group (<i>p</i> = 0.022) and a significantly lower catheter-based reintervention rate than that of the other two management groups (<i>p</i> = 0.011).</p> Conclusions <p>A management strategy using an initial definitive Rastelli operation or systemic-to-pulmonary shunt based on main pulmonary artery development and branch pulmonary arteries size is safe and effective for PA/VSD/PDA treatment. The staged TAP procedure could be a viable option for patients with PA/VSD/PDA and a well-developed main pulmonary artery segment.</p> Trial registration <p>Not applicable.</p>