ABSTRACT For distributed electrical power generation, linear engine-alternator systems have the potential to operate at high efficiency. They avoid the frictional losses present in rotating generators and enable the use of efficient combustion modes. However, their design and control optimization are matters of novelty. In this research, a single cylinder, two-stroke, free piston engine model has been built and simulated. The model describes the coupling between the piston motion dynamics and the chemical kinetics of the in-cylinder charge mixture undergoing homogeneous charge compression ignition (HCCI) combustion. The chemical kinetics reactions have been employed to find the net heat release rate and the start of combustion. Piston motion depends on the cylinder pressure as well as the dynamics of the mass-spring-damper system translator. For advanced investigations, the model results are represented by a multi-cycle simulation where 100 engine cycles were simulated with an average frequency of 125 Hz. At near-steady state conditions, the electrical generator converts 47% of the total fuel energy to electrical work at stoichiometric combustion conditions. It is shown that HCCI ignition timing strongly affects the performance of the engine. Combustion timing just before piston top dead center position encourages better engine stability and performance for the given model. The stability of the engine strongly depends on the rate of work done on the translator by the generator, putting the generator thrust force at the core of the engine control scheme. Cycle to cycle stability, with HCCI combustion occurring for each compression stroke, is achieved with the use of a modified proportional-derivative controller which alters the generator thrust force based on the cyclic change in the piston bottom dead center position. The research goal is to develop an optimized design with stable controls that yields a high efficiency conversion of chemical to electrical energy.