A method for controlling the flow rate of a pneumatic syringe in a system that includes a disposable fluid circuit and reusable hardware configured to accept the disposable fluid circuit. The disposable fluid circuit includes one or more syringes, while the reusable hardware includes a syringe pump for each syringe of the disposable fluid circuit and a controller. The syringe pump includes a vacuum/pressure source for moving the piston within the syringe and a position detector for indicating the position of the piston within the syringe. The method controls several distinct phases of the process: break pressure targeting, glide control and vent control, and the method is the same regardless of whether a positive pressure or a vacuum is applied to the piston of the syringe. Preferably, a proportional-integral-derivative (“PID”) feedback loop is used for controlling the movement of the piston in the syringe.