Generally, fuel cell (FC) power supplies cannot respond fast enough to dynamic load requirements. This research presents an energy management system for hybrid power sources in dc distribution systems. A supercapacitor (SC) module was designed to be the second power source in order to supply energy in transient, which can respond well to dynamic loads. In terms of circuits, a two-phase parallel boost converter was connected to each power source for regulating the output voltage. The interleaved technique was applied for reducing the current ripples of the sources. Flatness control, which is a nonlinear estimation technique, combined with a single-loop control strategy is proposed to control the system and it responds faster than multiple-loop controls. In this research, it included a hybrid system of two power sources namely a 500-W fuel cell emulator and a 165-F supercapacitor module, each connecting to a two-phase interleaved boost converter. The control algorithm for the hybrid system was developed and validated by the MATLAB-Simulink interfacing with a dSPACE 1103 controller card. The experimental results showed the rapid response of the proposed system to the dynamic load requirement. This confirmed that the single-loop flatness control is a potential algorithm that offers stabilization of the hybrid system.