In this study, we evaluated the flow characteristics of various types of waveguide-below-cutoff (WBC) arrays and their shielding effectiveness (SE) of electromagnetic pulses (EMP) based on computational fluid dynamics (CFD). Three types of waveguides were selected for analysis: (1) grid type, (2) honeycomb type, and (3) multi-layer types (2-ply, 4-ply, 6-ply, and 8-ply). To analyze the air flow characteristics, the flow velocities in the longitudinal center of the WBC and the differential pressures between the WBC array inlet and outlet were evaluated. Consequently, we derive the following conclusions: (1) despite an increase in the inlet velocity, the pressure drop of the 6-ply multi-layer type did not significantly increase as compared to that of other types of waveguides (waveguide thickness of 0.1 mm, SE of 100 dB); (2) the grid and honeycomb type had the fastest flow rate of 17.5 m/s, which is approximately 2.5 m/s faster than that at the inlet (waveguide thickness of 1 mm, module size of 30 mm); and (3) the average pressure drop of the grid type waveguide is the lowest in the overall model, whereas that of the 8-ply is the highest (waveguide thickness of 1 mm, module size of 30 mm, and SE of 80, 100 dB).