An air-fuel ratio control system for an internal combustion engine, which is capable of quickly and properly eliminating variation in air-fuel ratio between a plurality of cylinders. The air-fuel ratio control system 1 controls the amount of fuel to be supplied to first to fourth cylinders #1 to #4, on a cylinder-by-cylinder basis, thereby controlling the air-fuel ratio of a mixture supplied to each of the cylinders. A LAF sensor 14 delivers to an ECU 2 an output KACT indicative of the air-fuel ratio of exhaust gases emitted from the cylinders and merged. A cycle filter 23a and a rotation filter 23b filters the output KACT from the LAF sensor 14 such that components in respective bands of a first frequency fr1 and a second frequency fr2 are allowed to pass therethrough. A final fuel injection amount TOUT_i is determined, on a cylinder-by-cylinder basis, according to a first filtered value KACT_Fc or a second filtered value KACT_Fr such that the amplitude of the filtered value KACT_Fc or KACT_Fr converges to a predetermined value.