Combining Fuel Cell (FC) system with high power density Supercapacitors (SCs) leads to a system with a high efficiency, high performance and long lifetime. This paper compares two configurations for FC/SCs combination in Uninterruptible Power Supply (UPS). The objective is to present the power split between Fuel Cell and Supercapacitors hybrid system by MATLAB/Simulink software. The main criteria studied are system performance, lifetime and UPS cost.