Magnetic stimulation represents a compelling modality for achieving neuronal activation with high spatial resolution and low toxicity. Stimulation coils can be designed to achieve localized, spatially asymmetric fields that target neurons of a particular orientation. Furthermore, these devices may be encapsulated within biopolymers thereby avoiding direct metal/tissue interfaces that could induce chronic inflammation and glial scarring. Herein, we report a multiplexed microcoil array for localized activation of cortical neurons and retinal ganglion cells. We designed a computational model that related the activation function to the geometry and arrangement of coils, and selected a geometry with a region of activation <50 microns wide. We then fabricated SU8/Cu/SU8 tri-layer devices which were flexible, transparent and conformal and featured four individually-addressable microcoil stimulation elements. Interfaced with ex vivo cortex or retina slices from GCaMP6-transfected mice, we observed that individual neurons located within 40 microns of the element tip could be activated repeatedly and in a dose (power) dependent fashion. Taken together, these results highlight the potential of magnetic stimulation devices for brain-machine interfaces and could open new routes toward bioelectronic therapies including prosthetic vision devices.