Controlled auto ignition combustion mode has become a topic of major interest in recent years, mainly due to its potential in achieving high thermal efficiencies combined with significant reductions in NOx and soot emissions. However, expanding the controlled operation over a wide range of speeds and loads is a significant challenge, which must be addressed to achieve commercial success. Control analysis to date has been done by developing models which are engine specific, such models often rely on extensive parameters which are to be experimentally identified. Moreover, these models were valid only for a narrow operating range. In this paper, a detailed mathematical model of an HCCI engine, which is fuel flexible and valid for a transitions in engine speed, is developed based on ideal gas laws and basic thermodynamics and conservation principles. The different engine subsystems and engine phenomena are modeled in a “control-oriented sense” to address the combustion timing, peak pressure and heat release rate control issues. The outlined model is based on positive valve overlap strategy to achieve the exhaust gas recirculation, which is further attained via fully flexible valve actuation systems. The model is discretized into eight stages and later coupled together to yield final relationships between the outputs and inputs. The model has been implemented in MATLAB to facilitate simulation studies and requires minimum number of tuning parameters to be experimentally recognized. The results corresponding to different operating or control scenarios of an HCCI engine are subsequently discussed in detail. Model validation is based on two sets of engine data, obtained from literature. The validation suggests that the model, once tuned properly, shows a fair agreement between the simulation and experimental data for any given engine and most of the operating conditions.