Homogeneous charge compression ignition is a part-load combustion method, which can significantly reduce oxides of nitrogen (NO x) emissions compared to current lean-burn spark ignition engines. The challenge with homogeneous charge compression ignition combustion is the high cyclic variation due to the lack of direct ignition control. A fully variable electromagnetic valve train provides the internal exhaust gas recirculation through negative valve overlap which is required to obtain the necessary thermal energy to enable homogeneous charge compression ignition. This also increases the cyclic coupling as residual gas and unburnt fuel is transferred between cycles through exhaust gas recirculation. To improve combustion stability, an experimentally validated feed-forward water injection controller is presented. Utilizing the low latency and rapid calculation rate of a field programmable gate array, a real-time calculation of residual fuel mass is implemented on a prototyping engine controller. Using this field programmable gate array–based calculation, it is possible to calculate the amount of fuel and the required control interaction during an engine cycle. This controller prevents early rapid combustion following a late combustion cycle using direct water injection to cool the cylinder charge and counter the additional thermal energy from any residual fuel that is transferred between cycles. By cooling the trapped cylinder mass, the upcoming combustion phasing can be delayed to the desired setpoint. The controller was tested at several operating points and showed an improvement in the combustion stability as shown by a reduction in the standard deviation of combustion phasing and indicated mean effective pressure.