A fuel supply control system for an internal combustion engine having a throttle body, and a fuel injection valve arranged in an intake manifold upstream of the throttle body for supplying fuel to all cylinders. An air throttle valve has a valve body having a notched opening formed therein and disposed to be opposite the nozzle of the fuel injection valve to increase the flow speed of intake air in the vicinity of the nozzle when the air throttle valve is fully closed. An electronic control unit controls the fuel injection valve in response to operating conditions of the engine. The electronic control unit causes the air throttle valve to be fully closed when a predetermined low rotation-speed operating condition of the engine, in which at least the rotational speed of the engine is lower than a predetermined value, is satisfied. The predetermined value of the rotational speed of the engine is set such that the lower the atmospheric pressure the smaller the predetermined value.