In an internal combustion engine comprising a valve operating system connected to a pair of intake valves and arranged to open one of the intake valves only in a very small amount such that the one intake valve is brought into its substantially inoperative state, in a suction stroke mainly in a low speed rotation region of the engine, a fuel injection valve capable of injecting fuel toward a pair of intake ports independently corresponding to the intake valves, and a control means for controlling the operation of the fuel injection valve, the control means is arranged to control the fuel injection valve with a fuel injection completion time determined within a suction stroke, when the one intake valve is in the substantially inoperative state. This ensures that when the one intake valves has been brought into its substantially inoperative state, the injection of fuel by the fuel injection valve can be completed in the suction stroke, so that the injected fuel can be sequentially introduced into a combustion chamber in a condition of the other intake valve being open, thereby achieving an axially stratified air charge to provide an improved combustibility.