A lightning protection system (LPS) of an urban 110 kV substation is designed and analysed according to NFPA 780 and IEC 62305-3 standards. The analysis of the LPS is established on the value of risk assessment. The total area of the plant is described by one soil layer with uniform resistivity. This study aims to improve the understanding of an unexpected manner of the grounding system beneath lightning currents by clarifying the basic concepts of the lightning protection level and the new design procedure in this paper was clarified according to NFPA-780 level 1 for a lightning protection system. The program is integrated with the CDEGS software, which provides effective geometrical modeling with object and result visualization. Furthermore, module and automated fast Fourier transform (FFT) is implemented in this study to simulate electromagnetic fields in the time and frequency domains. These current values are compared to the desired protection levels within the standards. The study results show that for the improved protection of the system against lightning, the total power grid must be considered as a source of improvement for studying shielding influence and the protection levels provided inside this substation.