Previous clinical studies in pulmonary arterial hypertension (PAH) have concentrated predominantly on distal pulmonary vascular resistance, its contribution to the disease process, and response to therapy. However, it is well known that biomechanical factors such as shear stress have an impact on endothelial health and dysfunction in other parts of the vasculature. This study tested the hypothesis that wall shear stress is reduced in the proximal pulmonary arteries of PAH patients with the belief that reduced shear stress may contribute to pulmonary endothelial cell dysfunction and as a result, PAH progression. A combined MRI and computational fluid dynamics (CFD) approach was used to construct subject-specific pulmonary artery models and quantify flow features and wall shear stress (WSS) in five PAH patients with moderate-to-severe disease and five age- and sex-matched controls. Three-dimensional model reconstruction showed PAH patients have significantly larger main, right, and left pulmonary artery diameters (3.5 ± 0.4 vs. 2.7 ± 0.1 cm, P = 0.01; 2.5 ± 0.4 vs. 1.9 ± 0.2 cm, P = 0.04; and 2.6 ± 0.4 vs. 2.0 ± 0.2 cm, P = 0.01, respectively), and lower cardiac output (3.7 ± 1.2 vs. 5.8 ± 0.6 L/min, P = 0.02.). CFD showed significantly lower time-averaged central pulmonary artery WSS in PAH patients compared to controls (4.3 ± 2.8 vs. 20.5 ± 4.0 dynes/cm2, P = 0.0004). Distal WSS was not significantly different. A novel method of measuring WSS was utilized to demonstrate for the first time that WSS is altered in some patients with PAH. Using computational modeling in patient-specific models, WSS was found to be significantly lower in the proximal pulmonary arteries of PAH patients compared to controls. Reduced WSS in proximal pulmonary arteries may play a role in the pathogenesis and progression of PAH. This data may serve as a basis for future in vitro studies of, for example, effects of WSS on gene expression.