A plasma processing apparatus includes a processing chamber for processing a sample with a plasma, an RF power supply for generating the plasma within the processing chamber, an RF bias power supply for supplying RF bias power to a sample stage on which the sample is mounted, a pulse generation unit for creating first pulses for modulating the output from the RF power supply for generating the plasma and second pulses for modulating the output from the RF bias power supply, and a controller for providing control of the processing of the sample with the sample. The pulse generation unit creates the first pulses and the second pulses synchronized based on a pulse delay time transmitted from the controller. The pulse delay time is established to delay the second pulses relative to the first pulses.