This study aims to predict mechanical properties of scaffolds made of bioactive glass-carbon nanotube (CNT) composite through finite element analysis (FEA) and their permeability using computational fluid dynamics (CFD) simulations. We start with constructing a three-dimensional model for the complete scaffold using cleaned/denoised images obtained from microcomputed tomography. To save computational effort, a representative volume element (RVE) is carved out from this model such that geometric properties like porosity and tortuosity are preserved. FEA requires material properties for which we have assumed that the CNTs are uniformly dispersed and hence, the composite behaves as a homogeneous isotropic material whose mechanical properties are experimentally obtained from a standard specimen. FEA has been performed on converged mesh for the RVE to obtain the compressive strength of the scaffolds. These computationally obtained compressive strengths compared well with those obtained experimentally, justifying our use of a homogeneous isotropic material model. We repeat the comparison for another geometry fabricated using additive manufacturing and find similarities in computational and experimental results. Hence, the compressive strength of bioactive glass-CNT composite scaffolds can be nondestructively predicted from our bulk identified mechanical properties irrespective of the geometry. For the CFD analysis, fluid flow is simulated in the porous region of the RVE and the estimated permeability of the scaffold is found to be satisfactory for nutrient and oxygen supply. Our study suggests that computational tools can help gain insights into the efficient design of scaffolds by obtaining the geometry having the right balance between strength and permeability for optimum performance.