Abstract: A control system for a variable stroke free piston engine, sets the ignition timing as a function of measured piston velocity. This velocity proportional ignition system provides spark advance on a stroke by stroke basis as an aid to starting the engine. Ignition changes over to a piston position based system when the engine is running at steady state. Fuel injection occurs at either piston dead point or is set as a function of piston position. Fuel injection is suppressed during cycles were the ports are not uncovered. The control system can also regulate compression ratio based upon piston position or knock sensor data. The preferred control system includes a hybrid digital analog system which includes a microprocessor.