Use a product called "KILZ" that you paint over it then repaint the ceiling .If you do this in the right order it will not come through. Just paint it and it will always bleed through over time.
A fresh stain will be easier to remove than an older, set-in stain. Your first step should be to find and remove the source of the rust. You don't want your problem returning. As with all stain...
If the stain is dry and the ceiling, if papered, is still sound, then try using a "stain-blocker" paint. Most paint manufacturers produce such paints.* Do not use a water-based paint, such as...