Growing consciousness of the threat posed by man-made climate change has spurred government institutions, industry, and science to find clean fuels to power economic activity. Fuel cells powered by hydrogen are one of the steps in gaining clean energy. To improve the efficiency of the fuel cell, the hybrid solutions are required. This article shows a new approach to the design and control of a hybrid energy storage system for portable applications. The methodology allows us to optimize the desired physical parameters of the elements (weight or size) in order to withstand the connected load power demand. Such an approach allows us to minimize weight, which is essential in portable systems. The methodology was proven by building a technology demonstrator. The measurements of physical objects verified the electrical parameters received during simulation and allowed a lower weight of the system, compared to the system based only on Li-ion batteries.