Transcranial magnetic stimulation (TMS) to the cerebral cortex is a major in vitro technique that is used in the field of neurophysiology. The magnitude of the motor-evoked potentials (MEP) that are elicited by TMS to the primary motor cortex reflect the excitability of the corticospinal pathway. MEPs are very sensitive to the scalp location of the stimulus coil, especially when corticospinal excitability is recorded during walking or other dynamic motions. In this study, we created a coil navigational system that consisted of three-dimensional motion analysis cameras, rigid bodies on the head and coil, and programming software. In order to evaluate the feasibility of the use of our system, pseudo TMS was applied during treadmill walking with or without the navigational system. As a result, we found that the variances due to coil location and/or distance from the target site were reduced with our system. This technique enabled us to realize high precision and accuracy in coil placement, even during dynamic motion.