Homogeneous charge compression ignition has the potential to significantly reduce NO x emissions, while maintaining a high fuel efficiency. Homogeneous charge compression ignition is characterized by compression-induced autoignition of a lean homogeneous air–fuel mixture. Combustion timing is highly dependent on the in-cylinder state including pressure, temperature and trapped mass. To control homogeneous charge compression ignition combustion, it is necessary to have an accurate representation of the gas exchange process. Currently, microprocessor-based engine control units require that the gas exchange process is linearized around a desired operating point to simplify the model for real-time implementation. This reduces the models’ ability to handle disturbances and limits the flexibility of the model. However, using a field programmable gate array, a detailed simulation of the physical gas exchange process can be implemented in real time. This paper outlines the process of converting physical governing equations to an offline zero-dimensional gas exchange model. The process used to convert this model to a field programmable gate array capable model is described. This model is experimentally validated using a single cylinder research engine with electromagnetic valves to record real-time field programmable gate array gas exchange results and comparing to the offline zero-dimensional physical model. The field programmable gate array model is able to accurately calculate the cylinder temperature and cylinder mass at 0.1 °CA intervals during the gas exchange process for a range of negative valve overlaps, boost conditions and engine speeds making the model useful for future real-time control applications.