The current work is based on the computational design optimisation for a two-stroke, uniflow scavenging free piston engine prototype for use in series hybrid vehicles to reach high efficiency levels combined with low emissions. Here the performance goals have been attempted via Homogeneous Charge Compression Ignition (HCCI) Diesel combustion with increased levels of exhaust gas recirculation (EGR) and direct injection. For optimal mixture preparation and composition, a highly tuned gas exchange system is required and also adapted injection parameters are needed to induce heat release at around top dead center (TDC).A computational methodology has been developed based on iterations between zero-, one-dimensional and simplified Computational Fluid Dynamics (CFD) simulations to define the operating conditions and overall geometrical parameters which give the best engine performance. Based on these findings, more detailed three-dimensional CFD calculations have been used to specify the optimal intake and exhaust port configurations and injection characteristics. They also serve as a basis for validation of the performance results from the iterations. It is demonstrated that an indicated efficiency of above 50% and low emission levels for soot and NOx can be ensured via a high compression ratio, elevated EGR rates and HCCI combustion using direct injection and early injection timing.