In neonates requiring balloon aortic valvuloplasty, both anterograde and retrograde approaches are feasible. A recent comparison of these two approaches is lacking. A retrospective cohort study of neonates at a single center undergoing BAV from 9/00 to 7/14 was performed. Records were reviewed including pre- and post-intervention echocardiograms and catheterization data. Comparisons of acute efficacy and procedural safety were made based on type of approach utilized. Forty-two neonates underwent BAV. Eleven cases utilized exclusively an anterograde approach, while 31 included a retrograde approach (including 4 with both approaches used). There were no significant differences between groups in baseline demographic and clinical characteristics. Additionally, by both pre-intervention echocardiogram and catheterization, there were no differences based on approach in aortic valve gradient, degree of aortic insufficiency (AI), or degree of mitral regurgitation (MR). Both approaches were equally efficacious in gradient reduction (45 ± 17 vs. 44 ± 21 mmHg, p = 0.97), and there was no difference in post-intervention AI as assessed by both catheterization and echocardiogram (52% vs. 64% none or trivial, p = 0.74). Additionally, there was no difference in the proportion of patients with an increased severity of MR after BAV (15% vs. 22%, p = 0.52). The retrograde approach required a larger arterial catheter and was associated with a higher rate of arterial thrombosis (61% vs. 18%, p = 0.014). Both anterograde and retrograde approaches to neonatal BAV appear to be equally efficacious in the short term. The anterograde approach avoids the need for a larger arterial catheter and may reduce the risk of arterial thrombosis.