The post-fault high frequency currents caused by distribution capacitances are mainly observed as harmonics in the frequency domain for a transmission line. The paper discusses various influencing factors and proposes a natural frequency based protection scheme. The post-fault current spectrum is first analysed to find out natural frequency. And then the impedance based on the natural frequency is calculated and internal and external zone faults are distinguished via two criteria. The method is immune to the fault location and time. The method is validated by ATP and MATLAB simulation.