Regenerative properties of human mesenchymal stem cells (hMSC) can be enhanced by genetic modifications. Thus we aimed to develop a magnetic non-viral vector for microRNA (miR) delivery in freshly isolated hMSCs. miR/PEI/MNP transfection showed a better long term performance compared to miR/PEI transfection. Moreover magnetically modified hMSCs could be guided by an external magnet contributing to enhanced cell engraftment. Conclusively a magnetic non-viral carrier for efficient miR delivery in freshly isolated hMSCs was developed allowing specific control of stem cells and magnetic targeting.