A complexation extraction system was designed to develop a new process for the efficient removal of fluoride from solutions, such as zinc or copper electrolytes or wastewater derived from flue gas. The effects of the boron fluoride molar ratio, organic phase composition, initial pH, temperature, and phase volume ratio on the extraction efficiency were investigated. The extraction efficiency was found to increase with the increase in the boron fluoride molar ratio, Alamine336 concentration, and phase volume ratio, whereas it decreased with the increase in temperature. For the simulated electrolyte or wastewater derived from flue gas, the majority of metallic ions were insensitive to the extraction, with the exception of Al3+ and Fe3+. Fluoride decreased from 5 g/L to 0.05 g/L after two-stage cross-flow extraction alone; with an extraction efficiency of 99%. Both the stripping and cycling properties were excellent when sodium hydroxide was employed as the stripping reagent. Furthermore, the loading capacity was 43.4 g/L, and increased by four times, when boric acid was added. This novel process implies a wide range of potential applications, such as the removal of unwanted fluoride ions from various high-fluoride polluted solutions and the simplification of brine phase diagram.