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In this paper, a simulation model is proposed to evaluate the electromagnetic transient surge current distribution in a lightning protection system (LPS) due to a direct lightning stroke. The model is based on the coupled transmission line network in the frequency domain combined with the Fourier transform technique. The conductor of the LPS is described using the coupled transmission line model, and can be reduced to an active two-port equivalent circuit. The unknown quantities are the node voltages of the LPS at the physical junction, which leads to a fast solver at each frequency. The validation of the proposed approach is performed by comparing the results with those in the technical literature. The numerical examples show the flexibility, efficiency, and accuracy of the model in the range of practical application of LPS.