A system for controlling fuel flow in an internal combustion engine receives a command specifying a desired fuel flow rate from an electronic control module. The system generates a feedforward estimate of actuator current required to produce the desired flow rate. This estimate is combined with a fueling current offset value generated using a proportional-integral feedback controller. A differential pressure between the fuel rail and cylinder gas is converted, by surface interpolation based on a lookup table, to an estimate of actual fuel flow rate. The difference between this actual fuel flow rate and the desired flow rate is provided to the feedback controller as an error signal. The feedback controller preferably uses different gain values depending on an operating mode of the engine (speed control and torque control modes).