Objective We report a single-institute experience of neonatal transvenous radiofrequency pulmonary valve perforation for pulmonary atresia/intact ventricular septum, with echocardiographic predictors of biventricular circulation. Methods Data were reviewed retrospectively for all neonates who underwent primary transvenous pulmonary valve perforation for pulmonary atresia/intact ventricular septum between January 2008 and November 2018 at our institution. We compared patients who need systemic-to-pulmonary shunt or ductal stenting with patients who did not need. Results During the study period, 31 patients with pulmonary atresia/intact ventricular septum underwent successful radiofrequency pulmonary valve perforation and balloon dilation of the pulmonary valve. There was no procedure-related mortality. Sixteen patients (52%) needed systemic-to-pulmonary shunt or ductal stenting after initial procedure. Among the survivors (follow-up time of 1 to 11.5 years), 15 patients had a biventricular circulation and 6 patients had 1 and 1 forward slash 2 ventricular circulation. Two patients are awaiting for Fontan operation. Both the TV/MV annulus ratio (>0.85) and tricuspid valve z-score (>-1) were found to be a good predictor of a biventricular outcome in our cohort. Conclusions Percutaneous radiofrequency pulmonary valve perforation and balloon valvotomy is an effective and safe primary treatment strategy for neonates with pulmonary atresia/intact ventricular septum. Ductal stenting or systemic-to-pulmonary shunt may be required in the majority of patients who had smaller right heart components. Preselection of patients according to tricuspid valve z-score and TV/MV annulus ratio allows predicting biventricular circulation.