A stop control system for an internal combustion engine, which is capable of accurately stopping a piston at a predetermined position during stoppage of the engine while preventing occurrence of untoward noise and vibration. After stopping the engine 3, the stop control system 1 for the engine 3 according to the present invention executes a first stage control (step 34) in which a throttle valve 13a is controlled to a first stage control target opening degree ICMDOFPRE smaller than a second predetermined opening degree ICMDOF2, in order to stop the piston at the predetermined position, before executing a second stage control (step 42) in which the throttle valve 13a is controlled to the second predetermined opening degree ICMDOF2. Further, the stop control system 1 stabilizes initial conditions at the start of the second stage control by setting a first stage control start rotational speed NEICOFPRE and a first stage control target opening degree ICMDOFPRE according to a change in a corrected target stop control start rotational speed NEICOFREFN (steps 71 and 85).