Background: Little is known on the effect of epicardial fat in pulmonary arterial hypertension (PAH). Therefore, the present study sought to perform a comparative analysis on the influence of epicardial fat thickness (EFT) on the right and left ventricular function, between three different etiological varieties of pulmonary arterial hypertension: caused by congenital heart defects (atrial septum defects with left to right shunt), by systemic sclerosis, and by myocardial ischemia. Materials and Methods: This is a prospective observational study on 50 patients with documented PAH (systolic pulmonary artery pressure – PASP of >35 mmHg). The thickness of the epicardial adipose tissue was evaluated by 2D cardiac ultrasound, on the free wall of the right ventricle, during end-diastole, in the long parasternal axis view. The patients were divided into three study groups: Group 1 – PAH determined by congenital heart defects with left to right shunts (atrial septum defects, n = 25); Group 2 – PAH induced by systemic sclerosis (n = 12); Group 3 – PAH induced by myocardial ischemia (n = 13). Results: The average age was 54.48 ± 10.78 years, 30% (n = 15) of subjects were males, with a mean body mass index of 24.65 ± 4.40 kg/m2, EFT was 9.15 ± 2.24 mm, and the PASP was 41.33 ± 5.11 mmHg. Patients in Group 3 were more likely to smoke (p = 0.025) and presented a significantly lower LVEF, compared to the other groups (Group 1: 60% ± 6 vs. Group 2: 60% ± 7 vs. Group 3: 48% ± 7, p <0.0001). The largest EFT was found in Group 3 (11.08 ± 2.39 mm), followed by Group 2 (9.14 ± 2.03 mm), and Group 1 (8.16 ± 1.57 mm) (p = 0.0003). The linear regression analysis found no significant correlations between EFT and other echocardiographic parameters: PASP (r = –0.228, p = 0.118), LVEF (r = –0.265, p = 0.06), TAPSW (r = 0.015, p = 0.912), TEI (r = 0.085, p = 0.552), RVEDD (r = –0.195, p = 0.173), RA area (r = –178, p = 0.214), and LA diameter (r = 0.065, p = 0.650). Conclusions: Epicardial fat thickness was found to be significantly higher in patients with PAH induced by myocardial ischemia, followed by those with systemic sclerosis and congenital heart defects, respectively. EFT did not influence the echocardiographic parameters for left and right ventricular function in patients with pulmonary arterial hypertension of different etiologies.