The application of induced pluripotent stem (iPS) cells holds significant promise for regenerative medicine and drug screening. To produce sufficient quantities of high-quality iPS cells in undifferentiated form, a wave bioreactor has been widely used for static cell cultivation. A systematic optimization of shear stress and cell dispersion has been conducted using numerical simulation, as it is a powerful tool for obtaining accurate predictions in aggregated cell cultivation. In this study, the cells are modeled as rigid spherical particles initially distributed at the center of a square vessel. The simulation results indicate that the shear stress acting on the particles is proportional to the shaking speed and angle caused by the strong velocity gradient. Meanwhile, the characteristics of particle dispersion indicate that the particles are distributed efficiently in the whole tank under a larger shaking angle. An optimal condition for cell cultivation is proposed based on a specific analysis of the controlling parameters associated with the shaking velocity and angle. It is concluded that the numerical model and computer-aided design presented herein are powerful tools for the design optimization of a bioreactor for automated cell cultivation.