Previously, the authors have proposed the concept of piston trajectory-based combustion control enabled by free piston engines (FPE). With this novel control method, the FPE realizes in-cycle real-time combustion control, in terms of adjusting the ignition timing and manipulating the in-cylinder temperature trace, through various piston trajectories and achieves higher thermal efficiency compared to the conventional internal combustion engines. In this paper, the effects of this new combustion control on engine-out emissions are studied. First, a model is developed that includes different piston trajectories in the FPE, a convective heat loss sub model and a reduced n-heptane reaction mechanism with major emissions species from diesel engines. Afterwards, a new approach which reduces the engine-out emissions by employing novel piston trajectories is described. At last, analyses of the simulation results demonstrating the variable piston trajectories' effects on CO and NOx emissions are presented, which further reveal the advantages of the trajectory-based combustion control.