Branch pulmonary artery stenosis (BPAS) in the setting of systemic-pulmonary artery shunts (SPS) may result in significant sequelae. Limited information exists regarding the safety and efficacy of pulmonary artery balloon angioplasty and stent implantation via SPS in neonates and infants. This study aimed to examine the feasibility, safety, and efficacy of balloon angioplasty/stent implantation for BPAS performed via SPS in neonates and infants. A single-center retrospective analysis of all patients weighing 10 kg or less who underwent angioplasty for BPAS via SPS was performed. Systemic oxygen saturations and vessel diameter before, during, and after the procedure were compared. Between July 1996 and February 2008, 15 patients underwent 20 catheterizations for the treatment of 27 BPAS via SPS. The patients had a mean weight of 5.6 kg (range, 2.6-10 kg) and a mean age of 7.6 months (range, 7 days to 33 months). The SPS diameter ranged between 2 and 5 mm (median, 3.5 mm). Angioplasty was performed for all 27 lesions, and an additional stent was placed in 5 of these. The average lesion diameter increased from 2.3 ± 1.5 to 4.7 ± 1.7 mm (p < 0.05), and 25 (93 %) of the 27 lesions met the predetermined criteria for success. Systemic oxygen saturation increased from 73 ± 9.5 % to 82 ± 6.8 % immediately after intervention and was 83 ± 7.9 % at discharge (p < 0.05). There were no instances of shunt thrombosis. Two patients experienced transient hypotension during the procedure. No procedural deaths occurred. The study findings suggest that balloon angioplasty or stent implantation performed via SPS appears to be safe and effective treatment for BPAS in neonates and infants.