This article describes an axial transient vibration of a polygonal mirror scanner rotor driven by a flat-type brushless DC motor and supported by a passive thrust magnetic bearing and a radial air bearing. From results of theoretical and experimental investigations, the following characteristics of the vibration, countermeasures to suppress a static displacement, and the transient vibration have been deduced: (1) Repulsive magnetic force is induced between the stator coils and rotor magnet under current passage. The force is proportional to the motor current. The force causes axial static displacement and axial transient vibration. (2) Parametric investigation deduced that: (a) higher stiffness of the magnetic bearing and lower acceleration current linearly reduce both the static displacement and the transient vibration; however, the former may reduce lifetime of the air bearing due to a dry contact with start and stop operation, and the latter prolongs the startup time; (b) soft start-stop scheme of the motor current is effective to reduce the vibration.