The ionic compressor is a new and prospective technology applied for hydrogen storage which adopts a hydraulic system in which the hydraulic drive unit is a solid piston in the compression cavity. Controlling the trajectory of the solid piston is critical for achieving the designed thermodynamic process of compression. However, a strategy for controlling the position of a piston in an ionic compressor has not been reported in the open literature. In this paper, three valve-controlled methodologies are proposed for the effective control of a piston’s trajectory in an ionic compressor. A transient numerical model of the entire compression system was built using AMESim 2021 software. The performances of the proposed control methods were simulated and compared. The results show that the maximum isothermal efficiency, 50.28%, was obtained in the system using Position-P control, for which the highest hydrogen discharge mass for a single compression cycle of 1.14 g, a relatively low specific energy consumption of 2395.17 J/g, and a relatively small velocity control error of 0.32 m/s were observed. Although the lowest specific energy consumption was found in the case of the Dual-PS control method, the smallest mass product was also found for this case. Therefore, the Position-S control strategy was identified as the optimal method for a hydraulically driven ionic liquid compressor system.