To provide a stop control system for an internal combustion engine, which is capable of accurately stopping a piston at a predetermined position while compensating for variation in the stop characteristic of the piston and aging thereof. The stop control system 1 for the engine 3 according the present invention controls a throttle valve 13a toward an open side when an engine speed NE becomes lower than a stop control start rotational speed NEIGOFTH after the engine 3 is stopped (step 42), whereby a final compression stroke rotational speed NEPRSFTGT is controlled to a predetermined reference value NENPFLMTO, to thereby control the stop position of the piston 3d to a predetermined position. Further, the correlation between the stop control start rotational speed NEIGOFTH and the final compression stroke rotational speed NEPRSFTGT is determined (step 5, FIG. 9), and based on the determined correlation, a target stop control start rotational speed NEICOFREFX is calculate and learned (step 11), for use in the stop control.