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In this paper, we propose a protection scheme using a superconducting fault current limiter (SFCL) for the electric railway with traction power supply system with the automatic power changeover switch (ACS) system. The Korean electric railway uses a Scott transformer with many traction power substations. Each traction power substation has a neutral section. The ACS system is being installed at the neutral section and studied. In this system, shorting between the M- and T-phases prevents phase-to-phase faults, which was not considered for the conventional AC railway, due to the ACS. The proposed protection scheme using the SFCL mitigates this problem. In addition, we analysed the effect of the proposed protection scheme using the time-domain transient simulation software PSCAD/EMTDC.