Optimal operation of distributed energy resources (DERs) becomes one of the most critical aspects in the planning of microgrid systems as a result of energy policies aimed at increasing the integration of renewable energies, lowering fossil fuel use, and reducing the environmental effect. Due to the integration of a significant amount of renewable energy sources (RESs), the system inertia in such microgrids is reduced, which negatively affects frequency and voltage stability and weakens the microgrid. The use of Energy Storage Systems (ESSs) significantly lowers voltage and frequency variations. One of the most popular energy storage devices is the Flywheel Energy Storage System (FESS) which is used in this study to tackle the voltage and frequency variations. Among the benefits of FESS over other ESSs are its low maintenance costs, lengthy service life, lack of pollutants, high energy storage, quick charging, and limitless charge/discharge times. FESS has been controlled using a developed fuzzy logic controller that improves microgrid voltage and frequency. The studied power system model is implemented by the MATLAB/Simulink platform. The impacts of wind speed and load variations are examined in this study where voltage and frequency responses are compared in several scenarios. The proposed method displays a significant improvement in the voltage and frequency of the microgrid system. The obtained outcomes show that the fuzzy-controlled FESS is effective in reducing the voltage and frequency fluctuations of the studied microgrid system and keeping their values within the acceptable international standard limitation.