Magnetic stimulation of the nervous system, e.g. transcranial magnetic stimulation (TMS), has been used both to unravel basic structure and function of the nervous system as well as to treat neurological diseases, i.e. clinical depression. Despite progress in both areas, ongoing advancements have been limited by a lack of understanding of the mechanism by which magnetic stimulation alters neural activity. Here, we report responses of cortical neurons to magnetic stimulation arising from a sub-millimeter coil. Cell attached patch clamp was used to record neural activity of layer 5/6 pyramidal neurons of the prefrontal cortex (PFC) in the in vitro mouse brain slice preparation. The fields arising from the small coil were quite different from those arising during clinical TMS but nevertheless allowed the responses of cortical neurons to magnetic stimulation to be probed. For example, the focal nature of induced fields allowed the sensitivity of different regions within targeted pyramidal neurons, e.g. apical dendrite, soma and axon hillock, to be compared. We found that PFC pyramidal neurons were not sensitive to single pulses of stimulation regardless of coil location. However, regions of the apical dendrite and proximal axon were both sensitive to repetitive stimulation as long as the orientation of the induced electric field was aligned with the long axis of the neuron. These results suggest that neurons of the PFC are sensitive to weak magnetic fields and further, that this type of approach may be useful for unraveling some of the mechanisms underlying TMS.