Unplug the flat iron and allow it to cool completely. Dip a cotton swab in vinegar.
Dab the rust stains with the cotton swab. The acid in the vinegar breaks down rust and hard water spots. Don't allow vinegar to run inside the flat iron where it might damage electrical parts.
Rub the metal parts of the flat iron with fine steel wool to remove any remaining rust residue. Don't use steel wool on the ceramic pads because it can scratch the surface.
Dry the flat iron with a dry cloth. Store it away from the sink or moisture.