A closed loop pneumatic pumping system is provided. The system uses a gas compressor and a high pressure gas tank to exert pneumatic pressure against a reciprocating piston over a wellbore. The piston is connected to a rod string and downhole pump for pumping formation fluids from a wellbore. The system includes an electronic controller that controls movement, including pump speed of the piston as it cycles between upstrokes and downstrokes within a cylinder over the wellbore. In one aspect, speed is controlled by adjusting a speed of the compressor. In another aspect, speed is controlled by adjusting the position of an upstroke control valve and a downstroke control valve. In one aspect, the pump stroke controller is configured to adjust a speed of the upstroke and a speed of the downstroke in response to signals indicative of pump fillage. A method for optimizing pneumatic pumping speed at a wellbore is also provided herein.