In a fuel injection controller for a fuel injection system that executes an injection quantity learning operation for a fuel injection valve, a drive signal is outputted when the diagnosis condition is satisfied. An actual injection quantity of fuel that is actually injected by the fuel injection valve is computed. The fuel injection controller computes a correction amount based on a difference between the actual injection quantity and the command injection quantity. The fuel injection controller determines whether the correction amount exceeds a limit value. An injection deviation amount between the command injection quantity and the actual injection quantity of fuel, which is injected based on the drive signal corrected by the limit value, is computed when the correction amount exceeds the limit value.