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Current transformer (CT) saturation may cause the mal-operation or operating time delay of protection relays. In this paper, a new algorithm for the compensation of the distorted secondary current due to CT saturation is suggested. The secondary current can be expressed as the linear combination of sinusoidal and exponential signals, if no saturation occurs. The current can be expressed with an autoregressive (AR) model, which is the linear combination of previous samples. During saturation periods, the distorted current signal is compensated by the AR model using the data during the previous healthy section. Test results indicate that the proposed algorithm compensates the distorted currents accurately under a variety of fault conditions.