A lot of autonomous power systems have been designed and operated with different power levels and with special requirements for climatic conditions, availability, operation/maintenance cost, fuel consumption, environmental impacts, etc. In this paper a novel design of an autonomous power system with photovoltaic panels and electrochemical batteries for a shoreline electrode station is analyzed. This station will be constructed on the small island of Stachtoroi for the new high voltage direct current (HVDC) link of Attica–Crete in Greece. The general guidelines of the International Council on Large Electric Systems (CIGRE) and of the International Electrotechnical Committee (IEC) for the power system of lighting and auxiliary loads for these HVDC stations are supplied from the medium voltage or the low voltage distribution network, whereas they do not take into account the criticality of this interconnection, which will practically be the unique power facility of Crete island. The significance of Crete power system interconnection demands an increased reliability level for the power sources, similar to military installations and hospital surgeries. In this research a basic electrical installation design methodology is presented. First, the autonomous photovoltaic power system with the energy storage system (ESS) consisting of electrochemical batteries is preliminary designed according to the relative bibliography. The station power and energy consumption are analytically determined taking into consideration the daily temperature variation annually. Afterwards, a techno-economic optimization process based on a sensitivity analysis is formed modifying the size/power of photovoltaic panels (PVs), the type and the energy capacity of the batteries taking into consideration the operation cycle of PVs—batteries charge and discharge and the battery ageing based on the relationship between battery cycles—the depth of discharge, the daily solar variation per month, the installation cost of PVs and batteries, the respective maintenance cost, etc., while the reliability criteria of expected loss of load power and of load energy are satisfied. Using the proposed methodology the respective results are significantly improved in comparison with the preliminary autonomous power system design or the connection with the distribution power system.