In scaffold-based tissue engineering, sufficient oxygen and nutrient supply into cells within a scaffold is essential to increase cell viability and the proliferation rate. Generally, oxygen and nutrients reach the cells through the media by diffusion in vitro or in vivo, assuming there is no convection flow through a scaffold with small-sized pores. The scaffold diffusion rate depends mainly on the scaffold pore architecture. Thus, understanding the effect of scaffold pore architecture on the diffusion mechanism is necessary to design an efficient scaffold model. This study proposes a computational method to estimate diffusivity using the finite element analysis (FEA). This method can be applied to evaluate and analyze the effective diffusivity of a freeform fabricated 3D scaffold. The diffusion application module of commercial FEA software was used to calculate the spatial oxygen concentration gradient in a scaffold model medium. The effective diffusivities of each scaffold could be calculated from the oxygen concentration data, which revealed that the scaffold pore architecture influences its effective diffusivity. The proposed method has been verified experimentally and can be applied to design pore architectures with efficient diffusion by increasing our understanding of how the diffusion rate within a scaffold is affected by its pore architecture.