Frequency domain methods had been commonly used in power transmission line fault location. To improve the accuracy of frequency domain fault location methods, this paper studies a robust and accurate discrete Fourier transform (DFT)-based phasor estimation method. First, this paper analyses the deviation characteristics of DFT output phasors caused by decaying DC components with data window sliding. Based on these characteristics, this paper employs rotation factor computation to construct linear equations for the purpose of estimating the accurate fundamental frequency phasor during fault transient process. In this way, the accurate fundamental frequency phasor can be calculated by a two-step linear operation. Furthermore, to eliminate the effect of off-nominal frequency, the proposed method adjusts frequency deviation by using interpolation method. To further enhance the robustness for frequency domain fault location, the PauTa criterion is used to exclude the anomalous equations in the phasor estimation process. Finally, electro-magnetic fault simulation is used to evaluate the proposed method. The test results demonstrate that the proposed method improve the accuracy of fault location during the fault transient process.