Endothelial progenitor cells (EPCs) are of great importance in the process of endogenous blood vessel repair to maintain endothelial integrity and have been applied in a wide range of models of ischemic diseases. MicroRNAs represent a class of non-protein coding endogenous RNAs with 19–24 nucleotides in length and serve an important role in multiple physiological and pathological processes, including angiogenesis. It has been reported that miR-503 reduces angiogenesis in tumorigenesis. However, to our knowledge, the precise role of miR-503 in the regulation of EPCs remains unclear. In the current study, we found that the expression of miR-503 was decreased in mouse bone marrow derived EPCs under the hypoxic condition. Importantly, upregulation of miR-503 suppressed the proliferation, migration and capillary-like tube formation of EPCs induced by hypoxia. Furthermore, a dual luciferase reporter assay showed that Apelin, an endogenous ligand of the G protein-coupled receptor APJ, was a direct target of miR-503 and overexpression of miR-503 significantly inhibited the protein level of Apelin in EPCs. Moreover, hypoxia treatment enhanced the expression of Apelin in EPCs. Meanwhile ectopic expression of Apelin promoted cellular proliferation, migration and tube formation of EPCs in vitro. In summary, our results indicate that miR-503 regulates proliferation, migration and angiogenesis of EPCs by targeting Apelin.