Current traveling waves attenuation caused by ground distributed capacitance of long-distance transmission lines goes against the calibration of initial fault traveling wave arriving times, and arc sag increases location errors. To shorten double ends distance and ensure reliability of fault location under the fundamental frequency fluctuations, and improve its accuracy, this paper proposes a novel fault location scheme for transmission lines based on phase comparison with Kaiser self-convolution windows FFT. This scheme uses FFT program to solve the phase current fault component of multiple current measurements which are compared for determining fault selection; uses excellent sidelobe characteristics of Kaiser self-convolution window to restrain spectral leakage, then the reliability of phase comparison is increased. This paper theoretically analyzes the causes of the phase spectrum leakage, then elaborates the sidelobe characteristics, and finally, verifies the correctness of the proposed method by simulation. The results show that the proposed method can effectively suppress spectral leakage with a high reliability.