A method of adaptively predicting, during operation of a pump, a mass of fuel pumped by the pump during a pumping event to a fuel accumulator (“Qpump”) to control operation of the pump is provided, comprising: generating an adaptive model of operation of the pump, including estimating a start of pumping (“SOP”) position of a plunger of the pump, estimating Qpump, determining a converged value of the estimated SOP position, and determining a converged value of the estimated Qpump; using the adaptive model to predict Qpump by inputting to the model the converged value of the estimated SOP position, a measured pressure of fuel in the fuel accumulator and a measured temperature of fuel in the fuel accumulator; and controlling operation of the pump in response to the predicted Qpump.