In this study, to the aim was to design an isolated, reliable and efficient DC-DC (flyback based) photovoltaic energy sourced supply unit, which has its own electrolyte-super capacitor based energy storage unit in order to compensate for disruptions and failures that can occur in photovoltaic solar panels. In this storage unit, a hierarchical charging structure has been developed for eliminating the drawbacks of battery technologies such as cooling issues, chemical dangers, heavy weight, charging and discharging current/voltage limitations. The designed supply unit is capable of operating in a wide range of input voltages for the supply of important and expensive solar-based photovoltaic subsystems. Also, it was designed to supply a steady and balanced power to control systems that have microcontrollers or expensive control elements for different purposes up to 50 W. The design can be considered as a model for an uninterruptible power supply with a specific capacitive storage. The designed unit has important advantages due to its large usage area, especially microgrid and off-grid systems, its low cost and less complex construction. The designed hierarchical charging super capacitor based energy storage unit in this study is expected to have important implications for future research due to its possibility to be developed in accordance with different environmental conditions and objectives.