Overstroking in a linearly driven piston compressor of a cryogenic cooler may occur as a result of numerous factors, among which are: uncontrollable leaking of the working fluid from the compression into the bounce space, magnitude and asymmetry of the driving voltage, action of the gravity and g-forces, etc. The known solutions to a passive and active overstroking control are rather expensive, bulky and not always reliable. The authors report on the development of the novel approach to an overstroking protection, where instead of the piston position, the piston acceleration is evaluated using the analytical model of the linear actuator and a real-time measurement of the motor voltage and current, thus enabling for a convenient sensorless estimation of a direction and magnitude of the internal collisions. This eliminates the need in the dedicated position sensor and allows obtaining an observer which is insensitive to the environmental conditions (shock, vibration and temperature) and to the inaccuracies inherent in the regular sensorless observers. Based on this approach a full-scale controller was developed using the National Instrument real-time engine PCI 7030/6040E operating under the LabView software. From experimentation, the overstroking was practically eliminated in the wide range of the operational conditions without affecting the overall power consumption and cooling performance.