Background: Efficacy of current stem cell therapy needs to be improved. Poor homing efficiency is a one of the major limitation of current stem cell therapy. We evaluated novel priming strategy with magnetic nanoparticle to enhance homing of transplanted stem cell to target tissue. Methods: We harvested magnetic bionanoparticle from magnetic bacteria, AMB-1. Effects of magnetic nanoparticle on proliferation, viability, and migration of late human endothelial progenitor cells (EPC) were examined in vitro. Additionally, effects of magnetic nanoparticle on gene and protein expression related survival and adhesion were evaluated in EPC. Homing efficiency of EPC was evaluated in nude mouse hindlimb ischemia model. Results: Above threshold concentration, magnetic particle showed dose dependent detrimental effects on survival and proliferation of EPC. However below threshold concentration, magnetic particle transfection did not influence proliferation, survival of EPC and enhanced migration and trans-endothelial migration of EPC toward magnet. Transfection of magnetic nanoparticle did not influence on gene and protein expression related to survival, adhesion except mild enhancement of ICAM-1 expression in high magnetic particle concentration. High dose magnetic nanoparticle transfection enhanced homing of EPC in ischemic limb by magnet, compared to low dose magnetic particle transfection condition. Conclusion: Magnetic nanoparticle mediated homing strategy showed feasibility for application to stem cell therapy in vitro evaluation and enhanced targeted homing in vivo model. Magnetic nanoparticle guided homing can be a promising novel strategy to enhance efficacy of current stem cell therapy.