The Micro-Grid (MG) stability is a significant issue that must be maintained in all operational modes. Usually, two control strategies can be applied to MG; V/f control and PQ control strategies. MGs with V/f control strategy should have some Distributed Generators (DGs) which have fast responses versus load changes. The Flywheel Energy Storage System (FESS) has this characteristic. The FESS, which converts the mechanical energy to electrical form, can generate electrical power or absorb the additional power in power systems or MGs. In this paper, the FESS structure modeled in detail and two control strategies (V/f and PQ control) are applied for this application. In addition, in order to improve the MG frequency and voltage stability, two complementary controllers are proposed for the V/f control strategy; conventional PI and Fuzzy Controllers. A typical low voltage network, including FESS is simulated for four distinct scenarios in the MATLAB/ Simulink environment. It is shown that fuzzy controller has better performance than conventional PI controller in islanded microgrid.