Cyclosporine A (CsA) improved the success rate of transplantation. The CD26/dipeptidylpeptidase IV (DPP IV) system plays a critical role in mobilizing endothelial progenitor cells (EPCs) from bone marrow. This study investigated whether CsA manipulates CD26/DPP IV activity and increases EPC mobilization. C57 BL/6 mice were divided into control and CsA-treated groups. Before and after hindlimb ischemia was induced, circulating EPC number and serum levels of different cytokines were measured. Compared to the controls, CsA treatment significantly increased the blood levels of stroma-derived factor-1 and stem cell factor after ischemic stress (p < 0.001). The CsA group displayed a significant increase in the number of circulating EPCs (sca-1⁺KDR⁺ and c-kit⁺CD31⁺ EPCs, both p < 0.05). In vivo, CsA caused a significant increase in the numbers of EPCs incorporated into the Matrigel and ischemic limbs (p < 0.05). In the peripheral blood, CsA significantly decreased CD26⁺ cell numbers and attenuated the plasma CD26/DPP IV activity (p < 0.001). Furthermore, short-term CsA treatment significantly improved the perfusion of ischemic limbs and decreased the spontaneous digital amputation rate. In summary, CsA manipulates the mobilization of EPCs into the circulation via the CD26/DPP IV system. Short-term CsA treatment has beneficial effects on angiogensis of ischemic tissues.