The purpose of this thesis is to design an adaptive controller for Proton Exchange Membrane Fuel Cell. The objective of adaptive control scheme aims to maintain a desired steady voltage output under various loading conditions of fuel cell operation. First, an application of electro-chemical reactions of fuel cell results in a dynamic model, which is further simplified to a coupled nonlinear multi-input and multi-output system. Second, the linear recursive least square identification scheme is used to generate a 2nd order mathematical model of fuel cell. Based on the identification results, a SISO adaptive controller is designed and tested for the fuel cell. It is verified that the adaptive controller works successfully. At various fixed hydrogen flow rate, the voltage output has been well maintained under various current loads by adjusting the air flow rate.