Flow-electrode-based capacitive deionization (FCDI) is a desalination process that uses electrostatic adsorption and desorption of ions onto electrode materials. It provides a continuous desalination flow with high salt removal performance and low energy consumption. Since lithium has been regarded as an essential element for the last few decades, the efficient production of lithium from the natural environment has been intensively investigated. In this study, we have extracted lithium ions from aqueous solution by using FCDI desalination. We confirmed that lithium and chloride ions could be continuously collected and that the salt removal rate depends on various parameters, including feed-flow rate and a feed saline concentration. We found that the salt removal rate increases as the feed-flow rate decreases and the feed salt concentration increases. Furthermore, the salt removal rate depends on the circulation mode of the feed solution (continuous feed stream vs. batch feed stream), which allows control of the desalination performance (higher capacity vs. higher efficiency) depending on the purpose of the application. The salt removal rate was highest, at 215.06 μmol/m−2s−1, at the feed rate of 3 mL/min and the feed concentration of 100 mg/L. We believe that such efficient and continuous extraction of lithium chloride using FCDI desalination can open a new door for the current lithium-production industry, which typically uses natural water evaporation.