The objective of this study is to evaluate the safety and tolerability of the pharmacological treatment of pulmonary hypertension in pediatric patients. It is a retrospective, longitudinal, observational study on pediatric patients undergoing treatment with pulmonary targeted therapies. 63 patients were included (51 % male), with a median age of 3.4 years (IQR, 3.6 months–10 years) and a median weight 13 kg (IQR, 6–30 kg). Congenital heart disease was the etiology of pulmonary hypertension in the majority of cases (n = 33) and 28 patients were in NYHA functional class III–IV. The most commonly used drug was sildenafil (n = 79, 56 %), followed by bosentan (n = 27, 23 %), and a combination of both (n = 14, 41 %). 34 patients had adverse reactions (54 %) with an incidence rate of 1.02 per patient per year. The most commonly reported reactions were gastrointestinal symptoms (22 %) and spontaneous erections (22 %) in males. Nine severe adverse reactions (10 %) occurred, requiring eight treatment withdrawal and one hospital admission. Treatment with targeted therapies for pulmonary hypertension is safe in the pediatric population. Severe ADRs were uncommon both in monotherapy and in combination therapy. Combination therapy was associated with a higher rate of ADRs. We observed similar survival rates in children receiving sildenafil doses according to the European Medicines Agency (EMA) recommendations or higher.