Background Coarctation of the pulmonary artery may lead to its early obstruction. We investigated the outcomes of a strategy of aggressive reconstruction of the pulmonary arteries in the neonatal period. Methods From 2000 to 2013 a total of 162 consecutive neonates (< 90 days) underwent systemic-to-pulmonary shunting. Twenty-eight of them underwent the following concomitant reconstruction of the central pulmonary arteries: end-to-end anastomosis (4), patch reconstruction of the pulmonary arteries (24) with 0.4 mm Gore-Tex (W. L. Gore & Associates, Newark, DE) patch (18), or autologous pericardium (6). Ten patients were directed to univentricular palliation and 18 to biventricular repair. Results There was 1 in-hospital death (4%) and 2 deaths after hospital discharge (inter-stage mortality, 7%). The follow-up of the 25 survivors was complete. After a mean of 3 ± 3 years, patients with single ventricle palliation reached the following stages: shunts (2); one and a half ventricle repair (1); bidirectional cavopulmonary shunt (4); and Fontan (2). Fourteen of the patients destined for biventricular physiology reached complete repair while 2 patients were still with shunts. There was no pulmonary artery occlusion. Focal narrowing or pulmonary artery hypoplasia was the main indication for 10 of the subsequent 36 reinterventions. Conclusions Neonatal pulmonary artery reconstruction effectively prevents pulmonary artery occlusion and warrants pulmonary artery growth in the majority of cases of juxtaductal pulmonary artery coarctation. A number of these patients needed enlargement of their central pulmonary arteries in subsequent procedures. Indications of this reconstruction at the time of systemic-to-pulmonary shunting remains to be specified.