A control system for a high frequency oscillating ventilator (HFOV) includes an oscillator controller and a mean airway pressure (MAP) controller. The HFOV includes a reciprocating piston which is adapted to generate positive and negative pressure waves for delivery to a patient airway. The oscillator controller comprises a pair of closed loop control circuits including an oscillator pressure loop and a centering loop which are collectively adapted to regulate frequency and amplitude of piston reciprocations and centering of the piston. The MAP controller comprises a closed loop control circuit that is adapted for regulating MAP at the patient utilizing feedback in the form of patient circuit pressure. Likewise, the oscillator controller utilizes patient circuit pressure as well as piston displacement feedback in order to regulate movement of the piston.