This paper compares between responses of Fuzzy Logic Controller (FLC) based exciter and auto-tuning FLC based exciter. Both of the exciters are simulated separately with synchronous generator connected to infinite bus through a short transmission line. The systems where subjected to three phase fault at the infinite bus, maximum Integral of Square Error (ISE) of generator terminal voltage response and critical clearing time were taken as performance indices of the exciters. The systems then studied under normal operating condition to justify the need of auto-tuning.