Homogenous Charge Compression Ignition (HCCI) engines hold promise of high fuel efficiency and low emission levels for future green vehicles. But in contrast to gasoline and diesel engines, HCCI engines suffer from lack of having direct means to initiate combustion. A combustion timing controller with robust tracking performance is the key requirement to leverage HCCI application in production vehicles. In this paper, a two-state control-oriented model is developed to predict HCCI combustion timing for a range of engine operation. The experimental validation of the model confirms the accuracy of the model for HCCI control applications. An optimal integral state feedback controller is designed to control the combustion timing by modulating the ratio of two fuels. Optimization methods are used in order to determine the controller’s parameters. The results demonstrate the designed controller can reach optimal combustion timing within about two engine cycles, while showing good robustness to physical disturbances.