This study conducted a computational fluid dynamics(CFD) analysis to find an appropriate diameter or sectional area of air ducts and fluid pipes which have an electromagnetic pulse(EMP) shied to protect indoor electronic devices in special buildings like military fortifications. The result shows that the optimized outdoor air intake size can be defined with either the ratio of the maximum air velocity in the supply duct to the air intake size, or the shape ratio of indoor supply diffuser to the outdoor air intake. In the case of water channel, the fluid velocity at EMP shield with the identical size of the pipe, decreases by 25% in average due to the resistance of the shield. The enlargement of diameter at the shield, 2 step, improves the fluid flow. It illustrated that the diameter of downstream pipe size is 1step larger than the upstream for providing the design flow rate. The shield increases friction and resistance, in the case of oil pipe, so the average flow velocity at the middle of the shield increase by 50% in average. In consideration of the fluid viscosity, the oil pipe should be enlarged 4 or 5 step from the typical design configuration. Therefore, the fluid channel size for air, water, and oil, should be reconsidered by the engineering approach when EMP shield is placed in the middle of channel.