In spite of the increasingly stringent emission standards, the constant growth of road traffic contributes to climate change and induces detrimental effects on the environment. The European REWARD project (REal World Advanced Technologies foR Diesel Engines) aims to develop a new generation of Diesel engines complying with stricter post Euro 6 legislation and with lower CO2 emissions. Among the different technologies developed, a fuel-efficient two-stroke Diesel engine suited for C-segment passenger cars will be designed and experimentally evaluated. One major challenge for two-stroke engines is the achievement of an efficient scavenging. As the emptying of the in-cylinder burnt gases and the filling by fresh gases is performed in the same time, the complexity consists in removing as much as burnt gases as possible while avoiding the by-pass of fresh air toward the exhaust line. For the considered application, the uniflow scavenging architecture, which is featured by ports located in the bottom of the cylinder and valves in the head, is retained. Two possible arrangements for the intake and the exhaust are compared: either the standard configuration for which the intake is ensured by the ports and the exhaust by the valves or the reverse configuration. Both standard and reverse configurations are benchmarked by 0D system computations performed with LMS Imagine.Lab Amesim and by 3D CFD simulations with CONVERGE. The standard configuration is eventually preferred because the reverse configuration does not insure enough ISFC benefit, except for the high and full load operating conditions, and on the other side the achievement of an efficient scavenging is strongly penalized by the drag downstream the valves.