Introduction Conventional magnetic neurostimulation systems use a current-carrying coil to generate a time-varying magnetic field pulse, which in turn produces a spatially varying electric field in the nervous system. An alternative approach to generating the time-varying magnetic field is by means of moving permanent magnets. Several systems have been proposed, involving rotation of high-strength neodymium magnets. One of these systems, termed synchronized transcranial magnetic stimulation (sTMS), was explored as a treatment of major depressive disorder. In this work, we evaluate the electric field characteristics of sTMS using the finite element method. Methods The finite element model was implemented in COMSOL Multiphysics (COMSOL, Burlington, MA) using its version of the IEEE Specific Anthropomorphic Mannequin phantom. The head model (stator) has uniform, isotropic electrical conductivity of 0.33 S/m and relative permeability of 1. Three cylindrical magnets (rotators) are positioned along the midline: Magnet 1 is located over the frontal pole just above the eyebrows. Magnet 2 is 7.1 cm away from Magnet 1, approximately overlying the superior frontal gyrus. Magnet 3 is 9.2 cm away from Magnet 2, approximately overlying the parietal cortex. Each magnet is 2.54 cm in diameter and height, diametrically magnetized, with a residual flux density of 0.64 T. The axes of rotations are perpendicular to the sagital plane; and the rotation velocity is set to 10 Hz, corresponding to approximately peak alpha frequency. Results The electric field distribution of a single rotating magnet was first simulated in a sphere head model with radius of 8.5 cm. As the magnet rotates, the electric field switches from a figure-8 pattern (when the magnetic dipole is perpendicular to the head sphere at multiples of half-period) to a circular pattern (when the magnetic dipole is parallel to the head at multiples of quarter-period). The peak induced electric field strength at the surface of the head is approximately 0.05 V/m, in the direction parallel to the rotation axis of the magnet. The electric field distribution of the full sTMS configuration in the SAM head model shows broadly distributed over midline frontal polar, medial frontal, and parietal regions. The peak induced electric field strength at the surface of the head is approximately 0.06 V/m. At a depth of 1.5 cm from the head surface, corresponding to the depth of the cortex, the electric field strength attenuates to approximately 0.02 V/m. Conclusion We evaluated the electric field characteristics of the sTMS system of rotating magnets using the finite element method. We found that the maximum induced electric field strength at the level of the cortex is approximately 0.02 V/m, which is an order of magnitude lower compared to those delivered by transcranial current stimulation and low field magnetic stimulation. Direct electrophysiological data should also be collected to validate the proposed mechanism of action.