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A well-known frequency estimation algorithm using the linear prediction method is analyzed for flat fading wireless channels. The estimator outputs are statistically analyzed and its jitter performances are compared with the non-fading case and the Cramer-Rao bound. We provide a closed form solution for the distribution and the variance of the frequency estimates under fading conditions by making valid assumptions. We also verify the theoretical model using simulations. Analysis shows that the variance of the estimates for flat fading channels reaches a threshold point and increasing the transmit power does not necessarily improve the performances any further.