A control system for an internal combustion engine, which is capable of properly setting fuel injection timing according to the actual degree of delay of the amount of fresh air to be supplied to cylinders of the engine, thereby making it possible to positively suppress torque variation, when the control system has switched an air-fuel ratio mode between a lean mode and a rich mode. The control system controls the air-fuel ratio of a mixture by switching the air-fuel ratio mode. In the lean mode, the control system sets a target fresh air amount for the lean mode, and in the rich mode, it sets a target fresh air amount for the rich mode. Upon switching the air-fuel ratio mode, the control system corrects the fuel injection timing according to the difference between the target fresh air amount for the lean mode or the rich mode and the detected fresh air amount.