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Nowadays, many countries like to decrease their dependency on oil especially in energy generation. Fuel cell energy generation system is one of the most exiting techniques that have many advantages such as being clean, reliable, oil independent, ozone friendly, vibration free, movable and having high efficiency. For ensuring fuel cells correct operation, it is surrounded by many ancillary circuits which consume about 40% of its energy product. About 30% of this consumed energy uses by compressor which provides required air of system. Because of that, it seems wise to control and optimize the performance of compressor to maximize the output energy of system. Generally, compressors do not have any analytical formula, so their performance models by some characteristic charts or empirical formulas. Therefore, in controlling compressors, using model-based controllers may causes error and not be useful. In this case, fuzzy logic controller which is more robust than other conventional controllers can be good candidate. In this study, three fuzzy logic controllers are designed for controlling compressor performance. Matlab/Simulink toolbox is used to simulate system and study the accuracy and correctness of the system. The results show good accuracy of the designed controllers.