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In the use of orthogonal frequency division multiple access (OFDMA) in multiple access applications, symbols are transmitted in narrowband sub-channels, which are supposed to be orthogonal. However, the use of a practical oscillator, with its inherent drift because of temperature and other environmental changes, will result in clock jitter which destroys the orthogonality between subcarriers and introduces inter-carrier interference (ICI). To alleviate the problem, this study proposes a novel tracking-based estimation algorithm, using which the effect of clock jitter can be compensated. Instead of modelling the clock jitter as a white noise process, the authors present a more realistic coloured clock jitter model based on practical oscillators. Using the fact that the jitter is coloured and so the jitters in adjacent OFDMA symbols are very roughly related in a linear manner, the authors formulate a new algorithm that models the jitter in the most recent blocks as linearly time varying. The authors then make use of a new objective function based on this model to derive an iterative jitter tracking scheme, so that the jitter in the current block can be better tracked. Simulation results are presented to illustrate the improvement in performance that can be obtained.