A method to control a fuel injection system (1) for an internal combustion engine and provided with a fuel pump (4). The fuel pump (4) has: a pumping chamber (14); a piston (15) mounted so as to slide within the pumping chamber (14); an intake duct (17), which ends in the pumping chamber (14) and is provided with an intake valve (18); a delivery duct (19), which starts from the pumping chamber (14) and is provided with a delivery valve (20); and a flow rate adjustment device (6), which is coupled to the intake valve (18) and can be controlled so as to prevent the intake valve (18) from closing or allow it to close when a fuel pressure inside the pumping chamber (14) exceeds a fuel pressure in the intake duct (17). The control method presents the steps of: detecting when the internal combustion engine is stopped; and controlling, after the internal combustion engine has been stopped, the flow rate adjustment device (6) to allow the intake valve (18) to close.