Pulmonary valve (PV) balloon dilation (BD) is the primary therapy for infants born with critical pulmonary stenosis (PS) or membranous pulmonary atresia with intact ventricular septum (PAIVS). We observed left ventricular (LV) dysfunction in patients following BD and sought to determine its incidence, clinical course and associated risk factors. Clinical, echocardiographic and catheterization data for all patients who underwent neonatal (<2 weeks age) PV BD for critical PS or PAIVS between January 2000 and February 2014 were retrospectively analyzed (n = 129). Post-procedure LV dysfunction was defined as ejection fraction (EF) <54 %. Median age at PV BD was 1 day. Most (71 %) patients had critical PS. Median PV diameter pre-BD was 6.0 mm with PV z-scores −4.1 to 0.9, median LV EF pre-BD was 58 %. Post-BD LV dysfunction developed in 45 patients (35 %); 15 patients had LV EF ≤40 %. Median time to normalization of LV EF was 10 days (range 2–72). In univariate analysis, diagnosis (critical PS or PAIVS), right ventricle to LV pressure ratio pre-BD, acute procedural complication and post-BD inotropic support were not associated with post-BD LV dysfunction. In multivariable analysis, the predictors of post-procedure LV dysfunction were lower PV z-score (OR 1.81, p 0.04), tricuspid regurgitation pre-BD ≥ moderate (OR 3.73, p 0.008) and larger right ventricular apical area (OR 1.99, p 0.04). LV dysfunction post-neonatal PV BD develops in a significant number of patients (35 %) and can be severe, but resolves. The risk of developing LV dysfunction post-PV BD is highest in patients with larger right ventricles.