This apparatus is applied to an engine equipped with a fuel supply system that supplies pressure-increased fuel to a fuel injection valve, and performs the fuel injection from the injection valve in one combustion cycle by a multiple injection process that includes a pre-injection and a main injection that are executed with an interval therebetween. The apparatus calculates a deviation between a required value (one-dot chain line) and an actual value (solid line) regarding the end timing of the pre-injection, based on the manner of fluctuation of the fuel pressure in the fuel injection that is detected by a pressure sensor. A target main injection timing and a target pre-interval are individually set on the basis of the state of operation of the engine. Based on the deviation, the target main injection timing and the target pre-interval, the apparatus sets control target values regarding the execution period of the pre-injection.