A system for controlling fuel injection in an internal combustion engine such that when the target air-fuel ratio is switched from a rich value to a lean value, the air-fuel ratios are switched to the lean value by sequentially decreasing the amount of fuel injected into the cylinders, for example in a four cylinder engine into the #1, #2, #3 and #4 cylinders, with predetermined time differences. During this time, an electronic air control valve (EACV) is controlled in such a manner that it is stepwise opened with the switching of the air-fuel ratio s for the #1, #2, #3 and #4 cylinders, thereby causing the engine torque to remain the same to prevent the generation of a torque shock. When the target air-fuel ratio has been switched from the lean level to the rich level, the amounts of fuel injected into the #1, #2, #3 and #4 cylinders are controlled in such a manner that they are sequentially increased with predetermined time differences, and the EACV is controlled in such a manner that it is stepwise closed. Thus, it is possible to avoid the generation of a torque shock, while preventing the degradation of the emission during switching of the air-fuel ratio.