A stop control system for an internal combustion engine, which is capable of restarting the engine automatically stopped, in optimum timing, thereby making it possible to positively prevent occurrence of fogging of window glass of a vehicle compartment and improve fuel economy. The engine is connected to a compressor of an air conditioner. According to the stop control system, during idle stop, window glass temperature is calculated, and according to the calculated window glass temperature, limit humidity below which fogging of the window glass does not occur is set. When determining compartment humidity becomes equal to or higher than the limit humidity, the idle stop is terminated and the engine is restarted. When the weather is rainy or snowy, the determining compartment humidity is corrected. When vehicle compartment temperature is not lower than a first predetermined temperature, the window glass temperature is corrected.