A control apparatus in a magnetic levitation system for controlling attraction and/or repulsion forces created from a pair of electromagnets to levitate an object therebetween at a predetermined target position in a contactless manner, in response to a displacement of the object from the target position. The control apparatus includes a start/stop detector, a phase compensation circuit, an integrator, and a switching circuit. The start/stop detector detects a start and stop of a levitation control procedure and generates a control signal having a predetermined time duration when either of the start and stop of the levitation control procedure is detected. The compensation circuit provides a compensation signal to compensate AC currents flowing through the electromagnet so that the displacement of the object from the target position becomes zero. The integrator integrates the compensation signal. The switching circuit outputs the compensation signal when the control signal is not generated from the start/stop detector, and the integrated compensation signal when the control signal is generated. Therefore, the magnetic forces from the electromagnets to the object gradually varies at the beginning and ending of the procedure and hence the object is gradually levitated and seated.