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Motor cycles are one of the major sources of air pollution in crowded cities. In order to alleviate this problem, instead of the internal combustion engines new technologies such as pure PEM fuel cell system or hybrid system can be utilized. In this paper, a hybrid fuel cell system has been modeled and optimized. This system includes fuel cell stack, compressor, humidifier, pump, blower, hydrogen storage tank and chemical battery. After optimization, by using the Simulink software the system performance under the standard driving cycle (FTP75) has been simulated and the results of that have been compared with the non-hybrid system.