A fuel injection system designed to execute a learning operation to spray fuel through fuel injectors at each of given pressures of the fuel to determine the quantity of fuel sprayed actually from each of the fuel injectors (i.e., an actual injection quantity) into an internal combustion engine. The system calculates a deviation of each of the actual injection quantities from a target quantity to determine an injection correction value required to eliminate such a deviation. The system determines whether each of the injection correction values has an error or not and analyzes the mode in which the errors appear at the injection correction values to specify types of malfunction occurring in the system. The system relearns ones of the injection correction values as determined to have the errors.