A suitable scaffold architecture is always desirable to get a biomimetic scaffold for bone tissue engineering. In this regard, a fluid structure interaction analysis was carried out on different Micro-CTs (μCTs) and gyroids to observe the in vitro mechanical responses due to fluid flow. Computational fluid dynamics method was used to evaluate the permeability and wall shear stress (WSS), followed by a finite element method to obtain the mechanical stress within scaffolds. Different types of gyroids were designed based on the number of unit cells and porosity, where porosity of gyroids was kept same as μCTs. The main objective of the study is to examine the variations of permeability, WSS and mechanical stress with respect to the number of unit cells and porosity for different gyroids and μCTs. Mechanical responses were also compared between gyroids and μCTs. The results of this study highlighted that permeability and WSS of μCTs came close to the gyroids with eight unit cells but had significant differences in mechanical stress. The permeability of gyroids increased with the increase of porosity but decreased with the increase in number of unit cells. The opposite trend was shown in case of WSS within gyroids. This study will guide us in predicting an ideal scaffold for trabecular bone replacement.