Methods of reducing a registration error of a photomask are provided. A method of reducing a registration error of a photomask may include identifying the registration error with respect to a pattern element in a pattern region of the photomask. Moreover, the method may include reducing a thickness of a portion of a non-pattern region of the photomask by irradiating an energy beam onto a location of the non-pattern region of the photomask that is spaced apart from the pattern element, to generate stress at the pattern element. Related photomasks and methods of manufacturing an integrated circuit are also provided.