A stop control system for an internal combustion engine, which controls a stop position of a piston of the engine, is provided. An valve opening amount of an intake air flow rate control valve is determined based on the detected engine rotational speed and the detected crank angle after the ignition switch is turned off, and the intake air flow rate control valve is controlled so that the valve opening amount of the intake air flow rate control valve coincides with the determined valve opening amount. For example, the valve opening amount of the intake air flow rate control valve is determined according to the crank angle at the time the engine rotational speed decreases to reach a predetermined range, and the intake air flow rate control valve is controlled to be opened. With this control, the intake air amount of the engine is increased so that the stop position of the piston coincides with the desired position.