We have developed a facile purification method to obtain highly dispersed iron pyrite quantum dots (QDs) in chloroform, after a reaction by hot injection. The method is based on the electrophoresis of an immiscible phase-separated solution, a combination of the as-synthesized solution and chloroform. By applying a voltage between electrodes immersed in both solutions, the pyrite QDs are selectively transferred to chloroform. The obtained QDs are monocrystalline with an average diameter of ca. 5 nm.