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Combustion in HCCI engines depends on several parameters such as temperature, pressure, thermochemistry of the cylinder gases, etc. These variables affect the two significant combustion parameters: ignition timing and combustion duration. Controlling ignition timing and burn rate in such engines over a range of engine speeds and loads is an inherently challenging task. Existing single-zone HCCI engine-control models fail to accurately estimate the combustion parameters. Moreover, such models lacked the absolute dynamic control of all the valves. Although certain CFD based multi-zone models have been reported in literature, they are quite unwieldy for the development of fast and efficient HCCI-engine controllers. This paper outlines a physics-based two-zone model of an HCCI engine with an empirical mean burn duration model in order to better predict combustion parameters and facilitate controller development.