Organ-on-a-Chip (OoC) platforms hold promise for mimicking human physiology better than traditional methods. A vital aspect of OoC research is the investigation of oxygen distribution within these microscale systems as it affects cellular metabolism. Numerical simulations, valuable for this research, offer detailed insights into the interaction between physics, biology, and fluid flow. Nevertheless, in OoC research, many authors usually ignore the properties of hydrogels that mimic the human organs, e.g., their porosity and permeability, when numerical simulations are performed, due to the lack of information about these materials or difficulty in measuring them. However, simplifying these properties may sacrifice realistic aspects of the numerical results. In light of this, the present study aims to evaluate how hydrogel scaffolds within the OoC impact oxygen distribution, when simulated as porous media. For this purpose, computational fluid dynamic simulations of an OoC model were conducted through Ansys Fluent Software. Additionally, to qualitatively validate the current model, experimental fluid flow visualizations were conducted. The results showed that when a lower permeability is considered, the oxygen transport in the organ models occurs mainly by diffusion, while with a higher permeability, the oxygen transport occurs essentially by convection. Despite these differences, on average, the predicted oxygen concentration in the current setup was similar in both cases. The findings also indicated that for a lower permeability, the fluid velocity within the organ models is approximately zero. Moreover, the qualitative assessment demonstrated a strong agreement between the numerical and the experimental fluid flow in terms of flow streamlines.