Aim To investigate the effect of microRNA-126 （miR-126） on the proliferation and migration of endothelial progenitor cell （EPC） in the process of endothelial-to-mesenchymal transition （EndMT）. Methods Rat bone marrow-derived EPC was isolated, and then induced to mesenchymal cells by transforming growth factor-β1 （TGF-β1）. Overexpression of miR-126 was constructed in EPC by using lentiviral transfection. The proliferation of EPC was measured by using MTT assay, and migration was detected by using cell injury assay and Transwell assay. Results The transition of EPC from endothelial cells to mesenchymal cells was fully developed after 7 days treatment with TGF-β1 （5 μg/L） miR-126. MiR-126 inhibited the decrease of distance between injured EPC in the process of EndMT, and attenuated the cells per unit area on the bottom of membrane of Transwell. Conclusion MiR-126 inhibits the proliferation and migration of endothelial progenitor cells in the process of endothelial-to-mesenchymal transition.