A high voltage power supply system includes a DC-to-DC converter for producing a DC low voltage, a DC-to-AC inverter connected to a step-up transformer for producing an AC high voltage by transforming an AC low voltage obtained from the DC low voltage, and an inverter controller for controlling an operation time period of the DC-to-AC inverter longer than that of the DC-to-DC converter. Since a residual charge stored in a capacitor of the DC-to-DC converter is rapidly discharged by lengthening the operation time period of the DC-to-AC inverter, an unwanted AC high voltage is induced at a secondary winding of the step-up transformer.