This study presents a systematic framework for the real-time implementation of a new combustion control strategy—trajectory-based combustion control—for the operation of free piston engines (FPEs). The free piston engine is an alternative architecture of internal combustion (IC) engines, which does not have a mechanical crankshaft and hence allows extreme operational flexibility in terms of piston trajectory. The key idea of trajectory-based combustion control is to modulate the autoignition dynamics by tailoring the pressure and temperature history of the fuel–air mixture inside the combustion chamber, using the piston trajectory as the control input, for the optimal operation of the free piston engine. Here, we present the experimental investigation of trajectory-based combustion control using a novel instrument called controlled trajectory rapid compression and expansion machine (CT-RCEM) that can be used for studying a single combustion cycle of an internal combustion engine with precisely controlled initial and boundary conditions. The effect of the shape of the piston trajectory on the combustion phasing, combustion efficiency, and the indicated thermal efficiency has been found to be significant. The experimental results indicate that the trajectory-based combustion control is an effective strategy for combustion phasing control for FPE operation.