The risks associated with cardiac catheterization in children with pulmonary hypertension (PH) are increased compared with adults. We reviewed retrospectively all clinical data in children with PH [mean pulmonary artery pressure (mean PAp) ≥25 mmHg and pulmonary vascular resistance index (PVRI) ≥3 Wood units m²] undergoing cardiac catheterization between 2009 and 2014. Our strategy included a team approach, minimal catheter manipulation and sildenafil administration prior to extubation. Adverse events occurring within 48 h were noted. Seventy-five patients (36 males), median age 4 years (0.3–17) and median weight 14.6 kg (2.6–77 kg), underwent 97 cardiac catheterizations. Diagnoses included idiopathic or heritable pulmonary arterial hypertension (PAH) (29 %), PAH associated with congenital heart disease (52 %), left heart disease (5 %) and lung disease (14 %). Mean PAp was 43 ± 19 mmHg; mean PVRI was 9.7 ± 6 Wood units m². There were no deaths or serious arrhythmias. No patient required cardiac massage. Three patients who suffered adverse events had suprasystemic PAp (3/3), heritable PAH (2/3), decreased right ventricular function (3/3), and pulmonary artery capacitance index <1 ml/mmHg/m² (3/3) and were treatment naïve (3/3). No patient undergoing follow-up cardiac catheterization suffered a complication. In 45 % of cases, the data acquired from the follow-up cardiac catheterization resulted in an alteration of therapy. Three percent of children with PH undergoing cardiac catheterization suffered adverse events. However, there were no intra or post procedural deaths and no one required cardiac massage or cardioversion. Follow-up cardiac catheterization in patients receiving pulmonary hypertensive targeted therapy is safe and provides useful information.