In this study, a three-dimensional solid oxide fuel cell stack numerical model was developed and validated by experimental data. Five-cell SOFC stacks with different inlet and outlet manifold arrangement were investigated employing the numerical model. The stack polarization curve, current density, temperature, and flow distributions were analyzed. The results show that the effect of different manifold arrangement is almost neglected on the polarization curves and flow distribution. However, the current density and temperature distribution in individual unit of the stack can be influenced by the locations of inlets and outlets in the manifolds. Considering current density and temperature distribution uniformity as well as ease manufacturing and installation, the manifold arrangement with inlets at the top and outlets at the bottom for both fuel and air is recommended for SOFC stacks.