There has recently been a surge of interest in the properties and applications of monolayer protected clusters (MPCs). MPCs are metal nanoparticles that have unique optical, chemical, and electrochemical properties resulting from their small size. Because the size defines their properties, MPC particle size fractionation is important for control of the MPC characteristics for use in many potential applications. This paper explores the use of continuous free-flow electrophoresis (CFE) for the size fractionation of N-(2-mercaptopropionyl)glycine (tiopronin) monolayer protected gold clusters into monodisperse nanoparticle samples. CFE is a fractionation technique that isolates monodisperse particle sizes into several different collection vials on the tens of milligrams scale. This allows the MPCs to be separated based on their electrophoretic mobilities into isolated, monodisperse particles across a wide range of sizes. CFE separation of water-soluble tiopronin MPCs yielded fractions that varied in color, UV-visible spectra, transmission electron microscopy (TEM) size histograms, and solubility, indicating narrow size dispersity in the isolated fractions. UV-visible spectrophotometry verified the separation of the tiopronin MPCs through the inspection of surface plasmon resonance peak sizes for the different fractions. TEM was also used to verify the narrowed dispersity of MPC samples. The ability to separate water-soluble nanoparticles into 30 or more fractions in a continuous flow process will enable future studies on their size dependent properties.