Rapamycin is the most widely employed drug in drug-eluting stents. It has markedly reduced the risk of restenosis after coronary angioplasty. However, it caused late stent thrombosis through impairing the function of endothelial cells and delaying the re-endothelialization. Role of rapamycin in delaying re-endothelialization is complicated. This paper reviews the progress in research of the mechanism of suppressing the proliferation and migration of endothelial cells, attenuating the function of endothelial progenitor cells and inducing apoptosis of endothelial cells.