A new method of pilot protection based on S-transform sample entropy of current traveling wave for transmission lines is proposed, the ratio of S-transform sample entropy of fault current traveling wave at both ends of transmission line within a period of time after the occurrence of the fault is used to identify the internal and external fault. For the external fault, the forward traveling wave on the side and the backward traveling wave on the other side of transmission line are the same traveling wave, and the waveform is similarity, sample entropies of the corresponding current traveling wave are approximately equal to each other, so the ratio is close to one. For the internal fault, the forward traveling wave on the side and the backward traveling wave on the other side of transmission line are different, and the waveform is weak similarity, sample entropies of the corresponding current traveling wave have great differences, and the ratio is less than that of the external fault. According to these characteristics, a fault can be identified as internal or external one. The simulation result shows that the internal and external fault can be distinguished rapidly by the method presented in this paper, and its performance is not affected by fault types, fault inception angle, grounding resistance, fault location, and bus configuration.