The consumption of aquaculture products and, in turn, the importance of the aquaculture industry are increasing with the depletion of global fishery resources. In the flow-through aquaculture systems used in Korea, olive flounders are overcrowded near the central outlet, causing stress, and the sharp central outlet hole injures the olive flounders. Therefore, in this study, we propose a central outlet cap that can prevent overcrowding and injuries in olive flounders near the central outlet in a flow-through aquaculture system. An L27(35) orthogonal array was constructed using five central outlet cap design variables, and computational fluid dynamics (CFD) analysis was performed for each experimental point. The pressure drop between the tank inlet and the central outlet was evaluated, and the experimental point with the highest pressure drop was identified. In addition, the internal fluid velocity of the experimental point with the highest pressure drop value was confirmed to be improved compared to the initial flow-through aquaculture system. The central outlet cap designed in this study is expected to be economically beneficial to aquaculture by reducing the overcrowding of olive flounder and preventing injury to olive flounder while improving the internal fluid velocity.