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A phasor estimation algorithm based on the least square curve fitting technique for the distorted secondary current due to current transformer (CT) saturation is proposed. The mathematical form of the secondary current during CT saturation is represented as the scaled primary current with magnetizing current. The information on the scaled primary current is estimated using the least square technique, with the measured secondary current in the saturated section. The proposed method can estimate the phasor of a fundamental frequency component during the saturated period. The performance of the algorithm is validated under various fault and CT conditions using a C400 CT model. A series of performance evaluations shows that the proposed phasor estimation algorithm can estimate the phasor of the fundamental frequency component with high accuracy, regardless of fault conditions and CT characteristics.