Pulmonary atresia with intact ventricular septum (PA/IVS) is a rare cardiac congenital lesion characterized by imperforate pulmonary valve, intact ventricular septum, and atrial level shunt. Although different management strategies to establish a source of non-ductal dependent pulmonary blood flow have been described, studies have not assessed the relationship between the therapeutic approach, patient characteristics, and outcomes. The purpose of this study was to identify predictors of mortality for patients with PA/IVS. Neonates and children with PA/IVS were identified through analysis of the 2012 Kids’ Inpatient Database of the Healthcare Cost and Utilization Project. Hospital admissions that included a cardiac catheterization and/or surgical procedure were analyzed to identify demographics, co-morbidities, and outcomes. We identified 508 patients with PA/IVS with hospital admissions that included cardiac catheterization (n = 165), surgical procedures (n = 273), or both (n = 70). The incidence of mortality in this cohort was 6.69% (34/508). Univariable analysis demonstrated that age less than 12 months (p < 0.001), non-elective admission (p < 0.001), AKI (p = 0.001), sepsis (p = 0.002), and the use of ECMO (p < 0.001) were associated with an increased risk of mortality, while no difference was observed for the type of therapeutic approach (p = 0.498). These variables were used in a multivariable logistic regression analysis to develop the predictive model for mortality. Age less than 12 months, non-elective admission, and the use of ECMO in children with PA/IVS were predictors for mortality. Interestingly, the type of therapeutic approach did not influence mortality, which suggests that patient characteristics other than the method chosen to provide pulmonary blood flow determine mortality.