A fuel injection control system performs fuel injection for each engine cylinder at mutually different timings in each engine revolution cycle. First and former fuel injection is take place at a timing well advanced in view of a timing of opening of an intake valve of the corresponding engine cylinder to inject full amount of fuel derived on the basis of an engine load and engine speed. Second fuel injection is performed at a timing close to or within the intake valve open period for injecting an amount for compensating fuel amount to be increased depending upon increase of the engine load. In addition, acceleration enrichment upon engine acceleration demand is taken place by adjusting the fuel injection amount for second fuel injection.