Currently, according to conventional charge-discharge profiles, energy consumed in charging Capacitive Deionization (CDI) systems is always a function of different parameters (current used for charging, capacitance and current employed for discharging) making it difficult to separate the effect of these parameters on CDI performance and energy efficiency. Thus, energy efficiencies are strongly influenced by the current in the preceding charge or discharge stage of the process. We find consistently that this phenomenon, which to our knowledge has not been addressed in previous CDI communications, is much more intense when different currents are applied for each of the charging and discharging cycles. The investigation reported here provides a mechanistic analysis of the operational aspects of CDI and develops a new procedure that allows for a precise evaluation of performance and energy efficiency. Furthermore, the model developed here allows one to separate charge and discharge cycles, and therefore contributes to the possibility of defining an operational mode for real-world devices in which effective separation of deionization and regeneration steps needs to be implemented. This method of analysis could be useful not only for CDI but also for other electrochemical systems such as in secondary batteries and supercapacitors where charge and discharge are typically employed.