ENDURUNS is a European R&D project that consists in developing and demonstrating a long endurance sea surveying Autonomous Underwater Vehicle (AUV), powered by a hydrogen fuel cell, to perform seabed mapping, geological studies, surveillance, ocean search missions, mineral and mining exploration. The thesis was developed in the framework of this project in the company HYSYTECH. It is focused on the mechanical design of the fuel cell, figuring out challenges such as the design of the stack to fit a limited space, the heating and cooling process of some components in a sealed environment, setting up the system to guarantee neutral buoyancy and a stable barycenter, and finally, assuring the capability of the system to deal with the high pressures and the demanding seawater environment.