This paper presents a new two-terminal numerical algorithm for fault location estimation using the synchronized phasor in time-domain. The proposed algorithm is also based on the synchronized voltage and current phasor measured from the PMUs (Phasor Measurement Units) installed at both ends of the transmission lines. In this paper, the algorithm is given without shunt capacitance and with shunt capacitance using II -model and estimated using DFT (Discrete Fourier Transform) and LES (Least Error Squares Method). The algorithm uses a very short data window and classification for real-time transmission line protection. To verify the validity of the proposed algorithm, the Electro-Magnetic Transient Program (EMTP) and MATLAB are used.