A fuel injection system designed to execute a learning operation to spray fuel through a fuel injector in a cycle to calculate an average of actual injection quantities for correcting an injection duration so as to minimize a deviation of the average from a target quantity. The system samples the actual injection quantities for a given period of time made up of a first and a second time section. In each of the first and second time sections, the system decides whether each of the actual injection quantities is suitable for use in calculating the average or not. When a desired number of the actual injection quantities decided to be suitable for the calculation of the average has been derived in the first time section, the system proceeds to the second time section to calculate the average. This enhances the accuracy in determining the quantity of fuel actually sprayed from the fuel injector.