Solid oxide fuel cells are recognized as a promising energy conversion technology. Crucial to the field is the opportunity to reduce the costs of prototyping methodology. Due to the difficulty of conducting direct measurements inside the electrodes and fuel cell’s channels, numerical modeling remains the primary tool for improving the understanding and analyzing a fuel cell operation. Here, a computational fluid dynamic simulation of a banded solid oxide fuel cell’s stack, applied to enhance the geometrical design, is shown. A mathematical model, which includes momentum, heat, mass, and charge transport phenomena, was developed and used for the numerical simulation. The model was validated against the experimental study and confirmed its accuracy. The gas flow rate influence on the performance was investigated in details. Various arrangements of fuel and air channels were simulated and analyzed, including extending the system into a short stack. The proposed design modifications led to an increase in the volumetric power density of the stack compared to the existing prototype design. The proposed mathematical and numerical models were shown to be useful for testing further design modifications to the stack, including performance analysis, by changing the operating parameters of the system or applying new materials.