There are a number of ways you can do this using aftermarket kits made for this purpose. There are also a number of paints that are available in rust-color. However, if you want to use REAL rust, all you need is a nail and salt in a container of water! You don't need a lot, so you can use something like the cap from a spray can if you want.

Put enough water in the container to cover the nail, add a couple of tablespoons of salt and let it soak. You may want to stir it once in a while. When the water evaporates, you'll have rust! Just take a paint brush dampened with water and brush it on your model wherever you want the rust to be!