Sparse matrix converter (SMC) is an indirect AC-to-AC power electronic converter that has a fictitious DC link between rectification and inversion stages in which neither a capacitor nor an inductor, as the storage element, is utilized. Due to this advantage, SMC is used in AC drives, marine thrust systems, aerospace industry, as well as in wind energy applications. On the other hand, permanent magnet synchronous generator (PMSG) is competitive in wind turbine applications due to their prominent features. In this work, a fuzzy fractional-order PID (FFOPID) controller is designed for a PMSG based wind energy conversion system (WECS) which employs a three-phase three-level SMC. The FFOPID controller is chosen to combine the salient features of the fractional-order calculus and fuzzy logic operations to enhance the dynamic response of classical PID controller with fixed gains. The simulation results taken under different case studies are analyzed in detail, which demonstrate the superiority of the designed FFOPID controller over classical PID control approach in tracking d- and q-axis current references of the SMC at the output. With the designed control approach, the smooth control of the real and reactive power injections into the grid from the WECS are ensured with acceptable transient response.