► miR-21 expression was upregulated by rapamycin treatment. ► miR-21 deletion abolished rapamycin-induced inhibition on endothelial growth and mobility. ► RhoB was a direct target gene of miR-21. ► Knock-down of Raptor mimicked the augmentation of miR-21 induced by rapamycin. Rapamycin suppresses endothelial proliferation and migration, which leads to delayed re-endothelialization in the rapamycin-eluted stents that are used in coronary heart disease patients. Because microRNAs (miRs) play important roles in endothelial angiogenesis, we tested the hypothesis that rapamycin induces endothelial suppression, partly through pathways that involve miRs. Rapamycin treatment increased the expression of miR-21 in HUVECs. The downregulation of miR-21 by inhibitors abolished the negative effects of rapamycin on endothelial cell growth and mobility. RhoB was confirmed as a direct target gene of miR-21. Knockdown of Raptor by siRNA mimicked the effects of rapamycin on miR-21 expression. Our study provides a new explanation of the mechanism of rapamycin-mediated inhibition of endothelial proliferation and migration.