This paper investigates the influence of the non-uniform multi-stack design on the solid oxide fuel cell system size and performance. In this work a numerical solid oxide fuel cell model is developed and validated with the experimental data given in the literature. Numerical analyses are performed and the solid oxide fuel cell operation is simulated for the conventional single stack, uniform multi-stack and non-uniform multi-stack systems. Results show that the fuel utilization and therefore the efficiency of the system increases significantly for the multi-stack designs. Moreover, for the non-uniform multi-stack design the system size also decreases significantly. For the same operating conditions the efficiency and cell number values of the single stack, uniform multi-stack and non-uniform multi-stack designs are calculated as 9%/124 cells, 46%/256 cells and 46%/126 cells respectively.