Finding a stain on your ceiling is always a concern. It most likely means some kind of leak or moisture build up. First, you have to find the cause of the leak or moisture build up and fix it. Once that situation gets resolved, we want to make the ceiling look pretty again.
First thing to do is get some stain covering primer. Spray primer is recommended as it tends to work better on the ceiling than a brush. Then spray the ceiling, and let the primer dry. If the dried primer matches the color of the ceiling, the job is done. Otherwise, you may need to repaint your entire ceiling to get a matching color.