The incidence of COVID-19 infection in patients with pulmonary arterial hypertension (PAH) and chronic thromboembolic pulmonary hypertension (CTEPH) is similar to that in the general population, but the mortality rate is much higher. COVID-19 vaccination is strongly recommended for PAH/CTEPH patients. The aim of our cross-sectional study was to identify reasons why PAH/CTEPH patients refused vaccination against COVID-19. Moreover, we assessed the safety profile of approved COVID-19 vaccines in PAH/CTEPH patients. We examined 261 patients (164 PAH patients and 97CTEPH patients) with a median age of 60 (18–92) years, 62% of which were female. Sixty-one patients (23%) refused to be vaccinated. The main reason for unwillingness to be vaccinated was anxiety about adverse events (AEs, 61%). Age and fear of COVID-19 in the univariate analysis and age ≥60 years in the multivariate regression analysis were factors that impacted willingness to be vaccinated (OR = 2.5; p = 0.005). AEs were reported in 61% of vaccinated patients after the first dose and in 40.5% after the second dose (p = 0.01). The most common reported AEs were pain at the injection site (54.5%), fever (22%), fatigue (21%), myalgia (10.5%), and headache (10%). A lower percentage of AEs was reported in older patients (OR = 0.3; p = 0.001). The COVID-19 vaccines are safe for PAH/CTEPH patients. The results obtained in this study may encourage patients of these rare but severe cardio-pulmonary diseases to get vaccinated against COVID-19.