Abstract Advanced combustion, such as homogenous charge compression ignition (HCCI), requires precise control of the in-cylinder gas condition. Such advanced combustion does not always result in stoichiometric combustion; therefore, the changes in the oxygen concentration of the burned gas must be considered in the controller design. Furthermore, the changes in the oxygen concentration in the exhaust manifold are transferred to the intake manifold with delay. In this research, the transport dynamics of the exhaust gas recirculation (EGR) path were modeled by a pure time-varying delay and a second-order filter, and the model was used to estimate the oxygen concentration through the EGR valve. The feedforward controller was obtained based on the inverse model, which calculates the throttle and EGR valve positions based on the target values of the intake manifold pressure, EGR ratio, and estimated oxygen concentration at the EGR valve. The control performance of the proposed feedforward controller was evaluated by conducting simulations using both the mean value model and the precise model constructed using 1D simulation software.