Magnetic delivery system of mesenchymal stem cells (MSCs) has been developed for cartilage repair. It provides an effective and minimally invasive method for MSC transplantation. In this study, we evaluated the safety and quality of magnetically labeled human MSCs for practical applications. The safety of magnetically labeled MSCs was assessed using karyotyping, colony-forming assay using soft agar, and cell proliferation in a long-term culture. Magnetic labeling did not affect the karyotype, and MSCs retained their ability to grow and proliferate in an anchorage-independent manner even after exposure to magnetic force. The quality of the magnetically labeled MSCs was assessed by chondrocyte differentiation and reactivity toward magnetic forces. Magnetic labeling inhibited the chondrogenic differentiation of MSCs at higher densities of magnetic particles. MSCs labeled with ferucarbotran nanoparticles were retained by magnetic forces in a dose-dependent manner. The magnetization of MSCs with an appropriate density of magnetic particles maintained both qualities in MSCs. However, the uptake quantity of iron into MSCs varied across donors, even for the same density of magnetic particles. Therefore, the appropriate density of magnetic particles for use in MSC delivery for cartilage repair should be examined for every donor before treatment.