Hearing loss affects millions of people worldwide and often results from death of the sensory hair cells in the inner ear. Noise-induced damage is one of the leading causes of hair cell loss. Recently, the zebrafish lateral line system has emerged as a powerful in vivo model for real-time studies of hair cell damage and protection. In this research, we designed a microfluidic device to induce noise damage in hair cells of the zebrafish lateral line. As the first step, a 3-D computational fluid dynamics (CFD) simulation was utilized to predict the flow pattern inside the device. An ideal flow pattern for our application should feature higher velocity at the side and lower velocity in the middle of a channel. Flow induced from ordinary channel geometry with single inlet/outlet pair would not work for us because the boundary layers from the two side walls will grow and merge with each other and induce the maximum flow speed in the middle of the channel. In order to achieve the desired flow pattern, side-wall inlet/outlet pairs were used to suppress the growth of boundary layers. CFD simulation was used to design important parameters such as dimensions of the microfluidic channel and the angle of inlets and outlets. It was found that flow velocity at the side of the channel could be 6.7 times faster than the velocity in the middle when we array the inlets and outlets alternatively and set the angle of the inlet to 45° with 2.0 mm main channel width. This 3-D CFD model will serve as a convenient model to design a microfluidic device to induce noise damage in hair cells of a zebrafish lateral line by manipulating the flow pattern inside the device.