An in vitro, rat animal study was conducted. To assess the corticospinal axon growth potential in varying concentrations of neural progenitor cells (NPCs) and in magnetically localized labeled NPCs, quantitatively using our original organotypic coculture system. Transplantation of NPCs for spinal cord injury has been anticipated as a possible future treatment. It is important not only to illuminate the mechanism of NPCs for spinal cord injury, but also to develop an effective cell delivery system for clinical use. In order to develop more effective, efficient, and minimally invasive cell delivery systems, we established a new system using magnetic targeting. Magnetically labeled NPCs were suspended with activated magnetic beads and individual NPCs, and were compared the characterization to nonlabeled NPCs in vitro. We transplanted varying concentrations of 10, 10, 10, 10, and 10 NPCs in 1 microL medium to coculture models. Then the 10 labeled NPCs were transplanted with or without magnet to the cocultures. Magnetically labeled NPCs had similar potential in axon growth compared with nonlabeled NPCs, so there were few toxic effects of magnetically labeling NPCs. The differential potentials were not changed whether they were localized or scattered in vitro. Corticospinal axon growth was promoted in accordance with the transplanted NPC numbers around the organotypic coculture. Localized labeled NPCs with a magnet promoted axon growth much more than scattered labeled NPCs without a magnet, so magnetically localized labeled NPCs expressed higher potential in axon growth. Magnetically labeled NPCs, which were localized by magnetic force, could promote axon growth in this organotypic coculture system.