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Background: Critical pulmonary stenosis (PS) is one of the life-threatening congenital heart diseases which present during the neonatal period with cyanosis. Surgical valvotomy was once the procedure of choice for critical PS; however, balloon pulmonary valvuloplasty (BPV) has now become the standard treatment. Although the procedure is usually simple, crossing the pulmonary valve from the femoral vein can be difficult, especially when severe tricuspid regurgitation and right atrium dilatation are present. In such patients, the maneuver can be simplified by using the right internal jugular vein approach. However, many operators are reluctant to use this approach because of unfamiliarity with the technique, potential complications, and paucity of reports. Until now, there is no literature describing BPV using the transjugular approach in neonates, also none directly comparing the transfemoral and transjugular approaches. Objective: We compared transjugular with the transfemoral approach in terms of procedure time and complications. Materials and Methods: This was a retrospective cohort study. Participants were neonates with critical PS undergoing BPV in the National Cardiovascular Center Harapan Kita from 2013 to 2018. Results: Of 15 neonates undergoing BPV, eight were done using the transjugular approach and seven using the femoral approach. Mean age and weight in both groups was similar. In all eight patients using transjugular approach, crossing the pulmonary valve was consistently quick and easy. The total procedural time, pulmonary crossing time, and fluoro time was significantly shorter using the transjugular approach (65 ± 8 vs. 108 ± 17.8 min, P < 0.05; 22 ± 3.1 vs. 45 ± 14.8 min, P < 0.01; 29 ± 13 vs. 67 ± 35 min, P < 0.05). There were no complications relating to vascular access. Moreover, the BPV procedure itself demonstrated comparable results in both groups. Conclusion: BPV using the transjugular approach is safe and effective to relieve critical PS in neonates compared to the transfemoral approach.