Pulmonary arterial hypertension (PAH) is a common finding in patients with congenital heart disease (CHD), and has relevant prognostic implications. The recent introduction of advanced therapies (AT) considerably improved the clinical outcome of these patients, but real-world data are still lacking. We aimed at reporting the results of a long-term follow-up of CHD patients with PAH undergoing AT, followed at a tertiary Center during the two last decades. The study population included a total of 34 patients with an established diagnosis of CHD-related PAH. In addition to conventional treatment, 97% of patients started AT during the follow-up. Over a median follow-up of 9 [3-31] years, 11 (32.4%) patients died: 7 of them were affected by Eisenmenger syndrome and the majority of patients were in NYHA class ≥3 at the time of death. Among the 23 patients who were alive at the last follow-up, the majority were in NYHA class I-II. Oxygen saturation and 6-min walking distance improved in all subjects within the first 6 months after starting of AT. One patient with ventricular septum defect and high pulmonary resistances was successfully treated with AT to lower resistances and underwent defect closure. A good clinical outcome was also observed in the subset (n = 8) with Down syndrome. The results of this real-world experience suggest that, despite a relatively high mortality rate mostly related to late commencement of AT, the clinical outcome of subjects with CHD-related PAH undergoing AT are characterized by a good quality of life and clinical improvement in most patients.