This article offers a flatness theory-based energy management strategy (FEMS) for a hybrid power system consisting of a supercapacitor (SC) and lithium-ion battery. The proposed FEMS intends to allocate the power reference for the DC/DC converters of both the battery and SC while attaining higher efficiency and stable DC bus voltage. First, the entire system model is analyzed theoretically under the differential flatness approach to reduce the model order as a flat system. Second, the proposed FEMS is validated under different load conditions using MATLAB/Simulink. Thus, this FEMS provides high-quality energy to the load and reduces the fluctuations in the bus voltage. Moreover, the performance of the FEMS is compared with the load following (LF) strategy. The obtained results show that the proposed FEMS meet the real load power under fast variations with good power quality compared to the classical LF strategy, where the maximum overshoot of the bus voltage is 5%.