A control apparatus for an internal combustion engine where the inside of a combustion chamber is divided into a layer of internal EGR gas and a combustible layer to perform stratified combustion. In a port-injected engine equipped with first and second intake valves, the opening timing of the first intake valve is set before a top dead center (TDC) and the opening timing of the second intake valve is set after the TDC, and the closing timings of the first intake valve and the second intake valve are set after a bottom dead center. Then, fuel injection toward the first intake valve is started after the EGR gas, which was blown back to the intake port upstream of the first intake valve, is drawn into the combustion chamber after the top dead center.