This study proposes a new method for the design and performance verification of flight controller of MAVs using a magnetic suspension and balance system (MSBS), which is not only a non-contact type of balance but also a non-contact type of actuator. It can control the position and attitude of an experimental model and measure the external forces and moments acting on the model. It can also reduce or remove magnetic control forces or moments, which are used as constraint forces or moments during levitation, for specifically selected degree of freedoms (DOFs). A yaw controller for a flapping-wing MAV model was systematically designed using these advantages of the MSBS. The performance of the controller was verified under a free yaw condition; a free flight condition was emulated for the yaw DOF during a wind tunnel test while the magnetic constraint moment for the yaw direction was removed and the other positions and attitudes of the model were fixed by the MSBS.