A popular method for expanding human pluripotent stem cells (hPSCs). While stirring generates adequate fluid motions to lift the cells and facilitates mass transfers (of nutrients, dissolved gases, and metabolic wastes), excessive stirring could impose hydrodynamic forces deleterious for the growth of the cells. In this study, computational fluid dynamics (CFD) simulations were performed to first investigate hydrodynamic characteristics of fluid flows in a spinner flask, a common stirred suspension culture vessel used in laboratories. Flow patterns and distributions of shear stresses and the Kolmogorov length scales at varying impeller speeds were obtained. Comparison of the Kolmogorov length scales and sizes of hPSC aggregates, measured in the authors’ previous experimental study, showed a strong correlation between the two. In addition to the spinner flask which generated complex and transient turbulent flows, this study investigated a newly developed rotary wall vessel that had been designed to produce laminar, circular Couette flows in order to control shear stress. CFD simulations revealed significantly more uniform and homogeneous flows compared to those in the spinner flask.