A method and device provide simple positioning of a TMS coil relative to a coordinate system of the patient's head while allowing flexible positioning of the patient's head. The system includes a mobile console on a wheeled base that integrates various subsystems and supports a mast that, in turn, supports a coil gantry that supports a TMS coil assembly. The coil gantry includes a balance arm with a counterbalance and a halo assembly that connects to the coil. The coil gantry supports the weight of the coil and allows free movement of the coil in all dimensions for easy placement on the patient's head. A head support and coil alignment aligns the patient's head and holds the head in place relative to the coil during TMS treatment.