A system and method of controlling the hydraulic dwell time between a first injection and a second injection performed by a fuel injector of an internal combustion engine are disclosed, in which the injector is equipped with a needle operated by a control valve. A value of a nominal electric dwell time between the first injection and the second injection is determined. An actual instant of hydraulic closing of the fuel injector after the first injection is also determined. A corrected electric dwell time is calculated as a function of the nominal electric dwell time and the actual instant of hydraulic closing of the fuel injector after the first injection. The fuel injector is operated using the corrected electric dwell time.