In the preset study, a new identifier system has been proposed for optimal model estimation of Solid Oxide Fuel Cell (SOFC) stacks. To afford an appropriate identification system, the voltage-current profile of the system has been considered. The main idea is to minimize the Mean Squared Error (MSE) value between the actual output voltage of the stack and the output value achieved by the proposed model. Here, the MSE minimization has been established based on a new improved metaheuristic technique, called Fractional-order Social Network Search algorithm. The main advantage of the proposed technique is that it provides better trade-off between the global optimum and local optimum values. After system designing, it has been implemented to a studied case and its results are put in comparison with several latest techniques with considering two scenarios. One scenario with constant pressure and variable temperature and one other scenario with constant pressure and variable temperature. Final results indicate that the presented identification system provides satisfying results against the other compared methods in optimum system identification of the SOFCs.