Photovoltaic (PV) arrays are usually installed in open areas; hence, they are vulnerable to lightning strikes that can result in cell degradation, complete damage, service disruption, and increased maintenance costs. As a result, it is imperative to develop an effective and efficient lightning protection system by evaluating the transient behaviour of PV arrays during lightning events. The aim is to evaluate the transient analysis of large‐scale PV systems when subjected to lightning strikes using the finite difference time domain (FDTD) technique. Transient overvoltages are calculated at various points within the mounting system. To optimise the FDTD method's execution time and make it more suitable for less powerful hardware, a variable cell size approach is employed. Specifically, larger cell dimensions are used in the earthing system and smaller cell dimensions are used in the mounting system. The FDTD method is utilised to calculate the temporal variation of transient overvoltages for large‐scale PV systems under different scenarios, including variations in the striking point, soil resistivity, and the presence of a metal frame. Simulation results indicate that the highest transient overvoltages occur at the striking point, and these values increase with the presence of a PV metal frame as well as with higher soil resistivity. Furthermore, a comparison is performed between the overvoltage results obtained from the FDTD approach and the partial element equivalent circuit (PEEC) method at the four corner points of the mounting systems to demonstrate the superior accuracy of the FDTD method. Besides, a laboratory experiment is conducted on a small‐scale PV system to validate the simulation results. The calculated overvoltages obtained from the FDTD and PEEC methods are compared with the measured values, yielding a mean absolute error of 5% and 11% for the FDTD and PEEC methods, respectively, thereby confirming the accuracy of the FDTD simulation model.