Skeletal muscle injuries often leave lasting functional damage or pain. Muscle injuries are routinely treated conservatively, but the most effective treatment to promote the repair of injured muscles has not yet been established. Our previous report demonstrated that human peripheral blood-derived CD133+ cell transplantation to rat skeletal muscle injury models inhibited fibrosis and enhanced myogenesis after injury. However, the acquisition of a sufficient number of cells remains the limitation for clinical application, as the CD133 + population is rare in human blood. In this study, we applied a magnetic cell targeting system to accumulate transplanted cells in the muscle injury site and to enhance the regenerative effects of CD133 + cell transplantation, focusing on the fact that CD133 + cells are labeled with a magnetic bead for isolation. For the magnetic cell targeting, the magnet field generator was set up to adjust the peak of the magnetic gradient to the injury site of the tibialis anterior muscle, and 1 · 10 4 human peripheral blood CD133 + cells were locally injected into the injury site. This cell number is 10% of that used in the previous study. In another group, the same number of CD133 + cells was injected without magnetic force. The CD133 + cells transplanted with the magnetic force were more accumulated in the muscle injury site compared with the CD133 + cells transplanted without the magnetic force. In addition, the transplantation of CD133+ cells under the magnetic control inhibited fibrous scar formation and promoted angiogenesis and myogenesis, and also upregulated the mRNA expression of myogenic transcription factors, including Pax7, MyoD1 and Myogenin. However, the transplantation of CD133 + cells without the magnetic force failed to demonstrate these effects. Thus, our magnetic cell targeting system enables transplantation of a limited number of CD133 + cells to promote the repair of skeletal muscle injury.