Magnetic stimulation is able to modulate the neuronal network activity using the non-invasive magnetically induced current. However, it is unknown how stimulation modulates the neuronal network activity. Therefore, we considered that precise stimulation and evaluation of the modulation of network activities in the vicinity of stimulated sites is required. Here, to establish precisely magnetic stimulation, we developed a Mu-metal that has high magnetic permeability soft magnetic material based localized magnetic stimulation (LMS) system with micro-fabricated dual cell-culture chambers. And, combining this device with a microelectrode array (MEA) permitted the evaluation of the stimulus effects at the stimulated and non-stimulated sites. Here, the dual cell-culture chambers were arranged in a concentric circle manner. Between the inner and outer chambers, 4, 8 and 12 connecting microfluid channels were fabricated using polydimethylsiloxane (PDMS). Rat cortical neurons were separately cultured in outer and inner chambers. Through the micro-conduits, functional synaptic connections were formed. Mu-metal was aligned along the outer circle, which allowed us of focal magnetic stimulation to the cells in the outer chamber. Applying low frequency magnetic field to the Mu-metal, induced currents were generated and the electrical activity of the cells in the outer chamber was modified depending on the stimulation intensity. Following the modified activity in the outer circles, the cells in the inner chamber also showed slightly depressed activity patterns. These results suggested that our system would be promising for highly regulated neural stimulation.