This study aimed to compare long-term morbidity in patients with pulmonary atresia with intact ventricular septum (PA-IVS) treated with catheter-based intervention (group A) versus those undergoing heart surgery (group B) as initial intervention. Additionally, we conducted a systematic literature review on PA-IVS treatment. All neonates born in Sweden with PA-IVS between 2007 and 2019 were screened for inclusion. The inclusion criterion was decompression of the right ventricle for initial intervention. Medical records were reviewed, as well as the initial preoperative angiogram, and the diagnostic echocardiogram. Comparisons between groups were performed with Mann–Whitney U-test and Fisher´s exact test. A systematic literature review of original studies regarding treatment of PA-IVS (2002 and onward) was conducted following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines, to assess the outcomes of patients with PA-IVS. 34 (11 females) patients were included, 18 in group A and 16 in group B. There was no mortality in either group. Follow-up time ranged from 2 to 15 years (median 9). All attempted perforations in group A were successful, and 16 out of 18 patients reached biventricular circulation. In the surgical group 15 out of 16 patients reached biventricular circulation. The literature review presented heterogeneity in standards for treatment. This retrospective population-based multicenter study demonstrates that both catheter-based intervention and heart surgery are safe procedures. Our results are comparable to, or exceed, those in the systematic literature review. The systematic literature review displays a great heterogeneity in study design, with no definitive golden standard treatment.