The demand for sustainable and efficient power sources in underwater vehicles has led to increased exploration of alternative energy solutions. In this chapter, fuel cells, known for their high energy density and low environmental impact, are evaluated for their potential to provide continuous power for extended underwater missions. Additionally, two configurations of association with energy storage systems, including batteries and supercapacitors, are explored in terms of their energy storage capabilities and overall efficiency. To optimize energy utilization in underwater vehicles, a comparative analysis of these different configurations using rule-based energy management strategies is performed, combined with experimental power consumption data and high-fidelity simulation models. The comparative analysis aims to highlight the advantages and limitations of the association of fuel cells and energy storage systems to achieve the objectives associated with the context of unmanned and autonomous underwater vehicles. Ultimately, the findings contribute to the ongoing efforts to advance the field of unmanned underwater vehicle technology with a focus on enhancing energy efficiency and mission endurance.