Previous studies have demonstrated that activation of thrombin receptor could promote endothelial progenitor cell (EPC) migration. As cAMP-response-element-binding-protein-binding protein (CBP) is involved in many cellular biological processes, we hypothesized that CBP mediates thrombin-induced EPC migration. In this study, we examined whether CBP silencing would affect EPC migration induced by thrombin using small interference RNA approach. EPC isolated from the bone marrow of femurs and tibias of Sprague-Dawley rats were cultured and identified, and then were treated by thrombin alone or combined with CBP-shRNA lentivirus. Transwell chamber assay was performed to measure EPC migration. Quantitative real-time polymerase chain reaction and Western blot were carried out to detect the expression of CBP and CXCR4. Thrombin induced CBP expression in a time- and dose-dependent manner. Small interference RNA for CBP downregulated thrombin-induced CBP expression. Thrombin-induced EPC migration was also attenuated by CBP downregulation. Western blot indicated that CXCR4 expression on EPC is upregulated by thrombin and this effect was blocked by CBP silencing. In conclusion, thrombin-induced EPC migration was inhibited by CBP silencing via downregulation of CXCR4 expression, indicating that CBP plays an important role in thrombin-induced EPC migration.