Available energy optimization on permanently non-grid-connected systems is a critical task. In fact, optimizing the power consumption of the active subsystems is only a part of getting an increased autonomy. A full optimization cannot be done without taking into consideration the energy source and the energy storage system, whose efficiency directly effect the total system autonomy. In this paper we present the optimization of the energy storage system for an autonomous sail drone, based on the use of solar panels connected to backup batteries. The proposed study represents a significant use case, not only for the importance and the impact of the proposed sail-drone but also for the involved field application (autonomous self-propelled selfsustained system) which is finding an increasing number of different application and a strong interest among the scientific community.