Osteochondral tissue engineering aims to regenerate functional tissue mimicking physiological properties of injured cartilage and its subchondral bone. Given the distinct structural and biochemical difference between bone and cartilage, bi‐layered scaffolds and bioreactors are commonly employed. We present an osteochondral culture system which co‐cultured ATDC5 and MC3T3‐E1 cells on an additive manufactured bi‐layered scaffold in a dual‐chamber perfusion bioreactor. Also, finite element models (FEM) based on the micro‐computed tomography (μCT) image of the manufactured scaffold as well as on the computer aided design (CAD) were constructed; the microenvironment inside the two FEM was studied and compared. In vitro results showed that the co‐culture system supported osteochondral tissue growth in terms of cell viability, proliferation, distribution and attachment. In silico results showed that the CAD and the actual manufactured scaffold had significant differences in the flow velocity, differentiation media mixing in the bioreactor and fluid‐induced shear stress (FSS) experienced by the cells. This system was shown to have desired microenvironment for ostechondral tissue engineering and it can potentially be used as an inexpensive tool for testing newly developed pharmaceutical products for osteochondral defects.