In this work, electrophoresis was successfully used to separate three different polymer-coated magnetic iron oxide nanoparticles with similar sizes (nominally 50 nm) using high-pH borate buffer system. The coating polymers were dextran, polyethylene glycol, or carboxymethyl dextran. The results showed that the migration time of carboxymethyl dextran coated nanoparticles is the longest due to relatively more negative surface charges. Investigation of the effects of buffer concentration, pH, electric field strength and the capillary temperature, on electrophoretic properties of samples was also carried out. The results showed that pH, electric field strength and the capillary temperature had indirect relations with both of the migration time and the separation resolution of three different polymer-coated nanoparticles while the buffer concentration had a direct relation.