A fuel injection system for an internal combustion engine is provided which includes a fuel injector equipped with an actuator and a nozzle needle. The actuator works to lift the nozzle needle to inject fuel into an internal combustion engine. A controller controls an operation of the actuator to change an amount of lift of the nozzle needle a given number of times for a target injection duration, thereby ensuring the uniformity of size of atomized particles of the fuel sprayed from the fuel injector.