A nanoparticle separating apparatus that can separate nanoparticles from impurities in a nanoparticle dispersion, and a nanoparticle separating method using the same are disclosed. The nanoparticle separating apparatus according to an exemplary embodiment of the present invention includes: a body portion having an inlet hole into which a dispersion flows formed in one side thereof, an outlet hole through which the waste solution from which nanoparticles are separated flows formed in the other side, and a hollow channel formed between the inlet hole o and the outlet hole; a first electrode and a second electrode, each having a porous structure where a plurality of pores are formed, and at least one pair of the first and second electrodes being provided in the channel; and a power supply applying voltages, each having a different polarity, to the first electrode or to the second electrode.