The introduction of modern aftertreatment systems in marine diesel engines call for accurate prediction of exhaust gas temperature, since it significantly affects the performance of the aftertreatment system. The scavenging process establishes the initial conditions for combustion, directly affecting exhaust gas temperature, fuel economy, and emissions. In this paper, a semi-empirical zero-dimensional three zone scavenging model applicable to two-stroke uniflow scavenged diesel engines is updated using the results of CFD (computational fluid dynamics) simulations. In this 0-D model, the engine cylinders are divided in three zones (thermodynamic control volumes) namely, the pure air zone, mixing zone, and pure exhaust gas zone. The entrainment of air and exhaust gas in the mixing zone is specified by time varying mixing coefficients. The mixing coefficients were updated using results from CFD simulations based on the geometry of a modern 50 cm bore large two-stroke marine diesel engine. This increased the model’s accuracy by taking into account 2-D fluid dynamics phenomena in the cylinder ports and exhaust valve. Thus, the effect of engine load, inlet port swirl angle and partial covering of inlet ports on engine scavenging were investigated. The three-zone model was then updated and the findings of CFD simulations were reflected accordingly in the updated mixing coefficients of the scavenging model.