A magnetic bearing controller for controlling a magnetic levitation motor, the magnetic levitation motor including: a rotor; a pair of electromagnets that causes the rotor to levitate by electromagnetic force; an auxiliary bearing that supports a rotating shaft of the rotor when the rotor is stopped; and a rotor position detector that detects the rotor's position in a levitation direction. The magnetic bearing controller includes an operation current generator that generates an operation current value corresponding to a deviation between a position command value and the rotor's position detected by the rotor position detector. The operation current generator is configured to give a predetermined initial value greater than 0 to the operation current value at a start of levitation for causing the rotor in a state where the rotating shaft of the rotor is supported by the auxiliary bearing to levitate and be positioned at a predetermined target position.