A fuel injection system and method for injecting fuel for an internal combustion engine having fuel injection valves arranged on the upstream side and downstream side from the throttle valve respectively which consistently supplies an adequate quantity of fuel into the combustion chamber without fuel adhering to or remaining at the throttle valve, even when the throttle valve is abruptly enclosed. Based on plural parameters including the throttle opening θTH and the engine speed NE, the system includes means for determining the injection quantity of each of the upstream and downstream fuel injection valves, means for detecting a rate of change ΔθTH of the throttle opening in the injection-valve closing direction, means for stopping fuel injection of the upstream fuel injection valve when the rate of change ΔθTH is large, and means for reducing the injection quantity from the downstream fuel injection valve when the fuel injection of the upstream injection valve is stopped.