Cells cryopreservation is crucial for the treatment of several diseases, but the survival rate of the cells is significantly affected by the cooling process. Currently, programmable freezers based on liquid nitrogen technology are usually adopted but these solutions may cause the death of the cells due to undesired crystallization, membrane damage or osmotic shock. In the recent years, pulse tube refrigerators have attracted a lot of interest in many applications because of their intrinsic characteristics. Despite more gradual, the cooling rate of a similar refrigerator needs to be carefully controlled to meet the desired requirements of cells cryopreservation. Therefore, at the premises of Sapienza University of Rome a pulse tube-based prototype has been designed for cells cryopreservation and an experimental tests campaign has been conducted to assess the performance of the system for the scope. A new control logic, able to adjust the supplied voltage to electric heaters for the conditioning of the temperature inside the stand tubes, has been implemented and different configurations evaluated with cooling rate varying in the range 0.5 degrees C/min to 1.5 degrees C/min. The analysis has shown that the proposed control logic is able to cool down the stem cells in all the investigated range with a maximum temperature difference between the mean temperature of the tubes and the theoretical temperature of -7.65 degrees C for the configuration with copper plate and -4.09 degrees C for the configuration with aluminium plate which represents a safe condition. On the contrary, the copper plate allows approximating better the real cooling curve with the theoretical one and achieving a lower temperature variance at cooling rates higher than 1.25 degrees C/min. Although some further efforts are needed to tune the system up, the present work has demonstrated that a pulse tube refrigerator can be technically and commercially adopted as a viable solution for stem cells cryopreservation.