Electrode-based neural prosthetic implants that target the neocortex have the potential to treat a wide range of neurological and psychiatric disorders. However, their effectiveness has been limited due to their inability to selectively activate specific sub-populations of cortical neurons as well as the complex biological reactions that diminish the viability of electrodes over time. Magnetic stimulation is thought to overcome many of these limitations but coils small enough to be cortically implanted were not thought capable of neuronal activation. Here, we describe a new micro-coil designed for cortical implantation and demonstrate its effectiveness via a series of in vitro and in vivo experiments. A 50 x 100 µm sized micro-coil was designed and fabricated using silicon micro-fabrication technologies. In vitro experiments revealed that cortical pyramidal neurons in mouse brain slices could be strongly activated by the micro-coil stimulation without simultaneously activating passing axons. In vivo animal experiments showed that the micro-coils could be safely implanted into mouse cortex and could drive neural circuits in living animals. These results suggest that micro-coil implants may be an effective and reliable alternative to the existing electrode-based cortical implants.