The selection of busbar trunking systems is crucial for operational safety and reliability in electrical power systems. However, harmonic currents created by semiconductor-based converters reduce the current carrying capacity of busbar trunking systems, especially in electric vehicle charging stations, energy storage systems, microgrids, and data centers. In this case, busbar trunking systems with two neutrals or increased cross-section could be used for operating conditions with harmonic currents. Therefore, this study examines the thermal performance of the busbar trunking systems with different design parameters when loaded with harmonic currents. For this purpose, coupled electromagnetic field and thermal analyses were carried out using the finite element method. As expected, the results show that the maximum temperature in the temperature distributions increases significantly when busbar trunking systems are loaded with non-sinusoidal currents. Furthermore, the analysis studies determined the loading limits of busbar trunking systems within the thermal restriction when operating with non-sinusoidal currents. Accordingly, depending on the conductor’s phase sequences, the busbar trunking system model with one neutral conductor can be loaded with between 20% and 25%, two neutral conductors model can be loaded with between 22% and 39%, and the busbar trunking system model with 25% increased conductor cross-sections can be loaded with between 39% and 44% harmonic current. The results show that in the case of loading with non-sinusoidal currents, especially at a high portion of third harmonic components, choosing a busbar trunking system with a high cross-section area is advantageous compared to using two neutral conductors. This information is crucial to system reliability in electrical power system design. Therefore, it has become necessary to conduct these evaluations according to the equipment used while designing the electrical power system. • The proper selection of BTS is crucial for safety and reliability in power systems. • Magnetic and thermal analyses were carried out with the FEA for different BTS models. • Increasing the conductor cross-sectional area gives lower temperature rises. • These analyses are especially crucial for electric vehicle charging stations.