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In this paper, a detailed link level simulation has been studied and optimized to investigate the physical layer performance of Worldwide Interoperability for Microwave Access (WiMAX) IEEE 802.16e over AWGN and multipath Rayleigh fading channels, in which ITU-Reference channel models have been used. Two 802.16e based OFDMA transceivers have been designed by using MATLAB Simulink, the first one doesn't support channel estimation whereas the second does. Moreover, the effect of fading channel, Doppler shift and cyclic prefix on the system design performance has been analyzed and investigated. The bit error rate (BER) vs. bit energy-to-noise density ratio (Eb/No) curves was used to evaluate and compare the performance of QPSK modulation technique. The outcomes of simulation results clarified how the use of channel estimation improves the system performance, whereas obviously, the investigated system suffers from severe performance degradation and high probability of error whenever channel estimation is not applied.