An apparatus for and a method of controlling a fuel injection in which, in fuel injection control of an engine including a variable valve mechanism that can change an inlet valve opening characteristic, when an intake air amount is changed by an operation of the variable valve mechanism after the fuel injection valve performs first injection, a fuel amount corresponding to the change in intake air amount is injected in second injection after the first injection, and the sum of the fuel amount injected in the first injection and the fuel amount injected in the second injection becomes a fuel amount corresponding to an intake air amount fixed at an inlet valve closing timing.