Provided is a method and apparatus for preventing a transfer roller from being contaminated by toner in an image forming system, the method comprising determining a size of paper based on a time when front and rear ends of the paper are detected by a paper feeding sensor; comparing a size of an image formed on a photosensitive drum with the size of the paper; and if the size of the paper is the same as or smaller than the size of the image, determining a separation time of a transfer roller from a transfer belt in consideration of a delay time when the transfer roller is mechanically separated from the transfer belt after a separation command is applied to the transfer roller.