Previously, the authors have proposed the concept of piston trajectory-based combustion control enabled by free piston engines (FPEs). With this novel method, the FPE realizes in-cycle adjustment of combustion phase and real-time control of in-cylinder temperature and pressure through variable piston trajectories. As a result, higher indicated thermal efficiency, compared to conventional internal combustion engines (ICEs), is achieved. In this paper, the effects of this new combustion control on engine-out emissions are investigated. First, a comprehensive model is developed that includes different piston trajectories in the FPE, a convective heat loss model and a reduced n-heptane reaction mechanism with major emissions species. Afterwards, the chemical kinetics of CO and NOx emissions are described in details that reveal the feasibility of reducing engine-out emissions by employing novel piston trajectories. At last, analyses of the corresponding simulation results and comparisons of emissions and thermal efficiencies between the FPE and conventional ICEs are presented, which further shows the advantages of the trajectory-based combustion control. (C) 2016 Elsevier Ltd. All rights reserved.