Background: Endothelial progenitor cell play a vital role in neovascularization. Exercise-based cardiac rehabilitation significantly increases endothelial progenitor cells number and functions in patients with ischemic disease. Exercise can also increase the level of endothelial microRNAs. We hypothesized that microRNAs participate in regulating endothelial progenitor cell function under aerobic exercise. Thus, we attempted to identify such microRNAs and to verify the miR-126-3p target gene.Methods: Microarray is used to screen the microRNAs. The prediction programs TargetScan is used to predict the miR-126-3p target gene. Experimental EPCs are treated with miR-126-3p mimics. The relative expression of miR-126-3p and Mus musculus sprouty-related EVH1 domain-containing 1 (Spred1) are examined using real-time PCR and western blot. The dual-luciferase reporter assay is used to verify the miR-126-3p target gene.Results: The miR-126-3p target genes included those contributing to angiogenesis and revascularization. The predicted miR-126-3p target gene is Spred1. Compared with the control, miR-126-3p relative expression is highest following 48-h treatment with 50 nM miR-126-3 mimic. Spred1 mRNA and protein expression in the experimental group is 40.7% and 45.7%. The ratio of Renilla and firefly luciferase activity in the wild-type group is 88.3% and 74.2% of the control respectively (all, n = 3, p < 0.001).Conclusion: miR-126-3p participates in regulating endothelial progenitor cell function after aerobic exercise. MiR-126-3p inhibits the transcription and translation of Spred1, the target gene of miR-126-3p.