Introduction: Natural cancellous bone consists of inhomogeneous structures in which the porosity or pore size changes spatially. It becomes more challenging to exploit the potential of the designed scaffold to describe the complexity of bone architecture. In order to mimic cancellous bone architecture, a functionally graded scaffold (FGS) and uniform model based on pillar and hexagon unit cells have been successfully developed by using a Computer-Aided Design (CAD). This study aimed to determine the permeability of FGS and uniform scaffolds associated with the ability of cells to penetrate porous media. Methods: FGS and uniform scaffold were modelled based on the morphology of cancellous bone in bovine femoral condyle associated with porosity, Tb.Th, Tb.Sp, and BS/TV. The permeability and fluid movement through the scaffolds were analyzed using computational fluid dynamics. Results: The results show that the uniform scaffold has a strong correlation where the porosity increases, the permeability also increases. On the contrary, when the specific surface area increases, the permeability decreases significantly. When viewed on the scaffold PFGS and HFGS with 12NUC do not show a unique correlation, where the permeability value is proportional to the porosity level. Additionally, controlling NUC can be increasing BS/TV value. Conclusion: From the results explained in scaffold designing, it can mimic the morphology of cancellous bones such as Tb.T, Tb.Sp and BS/TV. It can be concluded that scaffold designed has fulfilled the requirements for the ideal scaffold because permeability value of the overall scaffold in the range of the cancellous bone.