In this study, the effects of varying the start of injection in a Free Piston Engine (FPE) have been investigated, using the KIVA-3V CFD code. In order to simulate the FPE the code has been modified by replacing the conventional crank shaft controlled piston motion by a piston motion profile calculated using a MATLAB/SIMULINK model. In this model, the piston motion is controlled by Newton's second law and the combustion process is represented by a simplified model based on ignition delay integrals and Wiebe functions. The results were tuned using predictions from the SENKIN software which are based on the detailed chemical kinetics mechanism of a Diesel oil surrogate represented by a blend of the main aliphatic (70% n-heptane) and aromatic (30% toluene) components. In order to help analyze the emission formation resulting from the HCCI/PPCI combustion modes in the engine, a special approach based on the temperature-equivalence ratio maps has been developed. Special attention was paid to predict a realistic initial flow field generated by ports and valves. The simulation results illustrate that by changing injection timing, the combustion process can be optimized, leading to high combustion efficiency and stable engine operation.