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Bioreactors enabling direct perfusion of cell suspensions or culture media through the pores of 3D scaffolds have long been used in tissue engineering to improve cell seeding efficiency as well as uniformity of cell distribution and tissue development. A macro‐scale U‐shaped bioreactor for cell culture under perfusion (U‐CUP) has been previously developed. In that system, the geometry of the perfusion chamber results in rather uniform flow through most of the scaffold volume, but not in the peripheral regions. Here, the design of the perfusion chamber has been optimized to provide a more homogenous perfusion flow through the scaffold. Then, the design of this macro‐scale flow‐optimized perfusion bioreactor (macro‐Flopper) has been miniaturized to create a mini‐scale device (mini‐Flopper) compatible with medium‐throughput assays. Computational fluid dynamic (CFD) modeling of the new chamber design …