The purpose of this study was to assess in pediatric pulmonary artery (PA) reconstruction candidates the feasibility and added utility of preoperative chest computed tomography angiography (CTA) using dual-energy technique, from which perfused blood volume (PBV)/iodine maps can be generated as a surrogate of pulmonary perfusion. Pediatric PA reconstruction patients were prospectively recruited for a new dose-neutral dual-energy CTA protocol. For each case, the severity of anatomic PA obstruction was graded by two pediatric cardiovascular radiologists in consensus using a modified Qanadli index. PBV maps were qualitatively reviewed and auto-segmented using Siemens syngo.via software. Associations between Qanadli scores and PBV were assessed with Spearman correlation (r) and ROC analysis. Effective radiation doses were estimated from dose-length product and ICRP 103 k-factors, using cubic Hermite spline interpolation. 19 patients were recruited with mean (SD) age of 6.0 (5.1), 11 (57.9%) female, 11 (73.7%) anesthetized. Higher QS correlated with lower PBV, both on a whole lung (r =  − 0.54, p < 0.001) and lobar (r =  − 0.50, p < 0.001) basis. The lung with lowest absolute PBV was predictive of the lung with highest Qanadli score, with AUC of 0.70 (95% CI 0.47–0.93). Qualitatively, PBV maps were heterogeneous, corresponding to multifocal PA stenoses, with decreased iodine content in areas of most severe obstruction. In conclusion, dual-energy chest CTA is feasible for pediatric PA reconstruction candidates. PBV maps show deficits in regions of more severe anatomic obstruction and may serve as a novel biomarker in this population.