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Flywheel energy storage (FES) has attracted new interest for uninterruptible power supply (UPS) applications in a facility microgrid. Due to technological advancements, the FES has become a promising alternative to traditional battery storage technologies. This paper aims at developing a tool to demonstrate the use of FES units for securing critical loads during a utility outage in a microgrid environment. The FES is modeled, simulated and evaluated in the MATLAB/SIMULINK® environment. A data center is used to represent a facility microgrid case study. It illustrates how an FES can help improve the load serving capability and provide a highly reliable ride-through capability for critical loads during a utility disturbance. In comparison with batteries, the application of FES for power security is new on the horizon. This limits the availability of experimental data. The simulation model presented in this paper will enable the analysis of short-term ride-through applications of FES during an islanded operation of a facility microgrid. As a result, it can provide a guideline for facility engineers in a data center or other types of facility microgrids to better design their backup power systems based on FES technology, which can be used in combination with traditional fuel-based generators.