A fuel system for an internal combustion engine includes a nozzle, a fuel pump, a spill valve assembly, and a pumping control unit. The spill valve assembly includes a first spill valve and a second spill valve fluidly in parallel between a plunger cavity in the fuel pump and a low pressure space. A pumping control unit commands closing of the first spill valve and then the second spill valve to adjust the spill valve assembly to start pressurization in the fuel pump, and commands opening the first spill valve to end pressurization in the fuel pump. A pumping duration is determined based on a timing of the commanded closing of the second spill valve and a timing of the commanded opening of the first spill valve.