Inflammation and dysfunction of circulating endothelial progenitor cells (EPCs) have been recognized as the possible factors for pulmonary hypertension (PH) progression, the present study determined that mesenchymal stem cells (MSCs) suppress inflammation associated down-regulation of circulating EPCs number and functions, and then exert therapeutic effects on PH. A single subcutaneous injection of monocrotaline (MCT) was used to induce a rat model of PH, and then administrated with MSCs transplantation. The therapeutic effects, including changes in hemodynamics and histology, and the plasma levels of TNF-alpha, the number and functions of circulating EPCs were evaluated. The results indicated that, the level of TNF-alpha in plasma was significantly increased in the model group compared with it in the control group. Moreover, the circulating EPCs number and functions were all significantly decreased, and the number of circulating EPCs was negatively correlated with the level of plasma TNF-alpha. Administration of MSCs transplantation could decreased the plasma level of TNF-alpha, and up-regulated the circulating EPCs number and functions, and then improved the pulmonary hemodynamic abnormality and vascular reconstruction effectively. Furthermore, the negative correlation between the circulating EPCs number and the plasma level of TNF-alpha could also be observed in the MSCs transplantation group. Thus, the present study suggested that transplantation of MSCs could attenuate MCT induced PH by improving pulmonary vascular repair probably via inhibiting inflammation mediated down-regulation of circulating EPCs.