A fuel injection system as set forth in clam 1, wherein when the number of times the injection quantity-use decision function has excluded the one from calculating the average through the average calculating function has reached a given value, said injection controller decides that the injection quantity determining function should be re-executed to instruct said fuel injector spray the fuel in a subsequent cycle and re-executes the injection quantity determining function to determine an actual injection quantity again, and wherein the injection quantity-use decision function makes the decision on the actual injection quantity, as determined in the subsequent cycle, in the first and second time sections.