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DC microgrid systems have been increasingly employed in recent years since there is a need to reduce the use of fossil fuels for electricity generation. Distributed generations (DGs), which are mostly DC sources in nature, play an important role in effective microgrid energy management systems. A key component in a microgrid system that can enhance stability and reliability is the employment of energy storage systems (ESSs). Nonetheless, ESSs currently lack cost-effectiveness. Each technology of the ESSs has been used for a particular purpose. Therefore, hybridization of different technologies can improve microgrid stability and reliability, as well as extend the ESS’s lifetime. This paper proposes to optimize the capacity and cost of a hybrid ESS between a battery and a supercapacitor in a standalone DC microgrid by calculating the cut-off frequency of a low-pass filter (LPF). The high fluctuation component of renewable power generation and load demand is supplied by the supercapacitor, while the low fluctuation component of renewable power generation and load demand is provided by the battery. A meta-heuristic strategy known as the Whale optimization algorithm (WOA) is applied to minimize the designed objective function, considering the total net present value (NPV) and replacement cost of the hybrid ESS, using the MATLAB environment. Real PV power, wind turbine power, and load demand are utilized for the analysis. The obtained results show that the reduction of power fluctuation for the battery in the DC microgrid can reduce the cost of the hybrid ESS. The microgrid system with only a battery has an <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">NPV<sub>total</sub></i> of $6,153,059, whereas the hybrid ESS has an <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">NPV<sub>total</sub></i> of $5,413,846. Thus, the hybrid ESS can reduce the total cost of the entire project by 12.01% compared to the system having only a battery. Consequently, the total system life-cycle cost of the hybrid ESS is lower than that of the battery-only system.