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Specialized physical and medium access control layer operations of WiMAX introduce a challenging problem to formulate a precise cross-layer analytical model for its capacity estimation. Although the cross-layer formulation is yet to be attempted in the literature, it can effectively serve as a fast and cost-effective tool to facilitate future deployment planning, efficient network maintenance, etc., and thus can expedite to cope up with the recent blast in WiMAX deployment. Therefore, we propose a novel formulation of cross-layer analytical model for WiMAX capacity estimation in this paper. Our formulation addresses intricate interrelationships between different layers in a protocol stack. Besides, the formulation separately addresses both reliable and unreliable transport layer transmissions. We verify our formulated model using ns-2 simulation, which reveals that the model can estimate the capacity of a WiMAX network with as low as 1% average error having a standard deviation of only 1%. Consequently, we find that the proposed model can achieve up to a 97% decrease in the average error compared to other available analytical models in the literature. Finally, we present different applications of the proposed model by utilizing it in network planning and protocol overhead analysis.