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Charging and discharging methods of lithium-ion battery installed in a power compensator for a DC railway system are developed in this paper. The power compensator has been developed to reduce its line voltage fluctuation caused by powering and braking trains. A number of charges and discharges deteriorates the lithium-ion battery and reduces the efficacy of the compensator. The proposed methods reduce the number of charges and discharges for prolonging the battery life by an insertion of a lowpass filter to the control circuit. The control method with the filter reduces the number of charging and discharging by 34%. Although the efficacy of the line voltage stabilization to rapid voltage change is decreased by the method, a parallel operation with an EDLC unit, whose capacity of 3% to that of the battery, complements the stabilization. The operations of the proposed methods are confirmed by numerical simulations using the electromagnetic transients program (EMTP) and by experiments using a scaled model.