This paper proposes a design methodology for an active power filter (APF) system to suppress the second harmonic subgroup injected by an AC electric arc furnace (EAF) to the utility grid. The APF system is composed of identical parallel units connected to the utility grid via a specially-designed coupling transformer. Each APF converter is a three-phase three-wire two-level voltage source converter (VSC). The number of parallel APF units, coupling transformer MVA rating, and turns ratio are optimized in the view of the ratings of commercially-available high voltage (HV) IGBTs. In this research work, line current waveforms sampled at 25.6-kS/s on the medium voltage (MV) side of a 65-MVA EAF transformer are then used to extract the second harmonic subgroup, 95-, 100-, and 105-Hz current components, by multiple synchronous reference frame (MSRF) analysis, which was previously proposed to decompose EAF current interharmonics and harmonics in real-time. By summing up this digital data of the second harmonic subgroup, the reference current signal for the APF system is produced in real-time. A detailed model of the APF system is then run on EMTDC/PSCAD to follow the produced reference current signal according to hysteresis band control philosophy. The simulation results show that the proposed APF system can successfully suppress the second harmonic subgroup of an AC EAF.