It could be any one of the several muscles that attach to the shoulder and all the way up to the skull. It could be referred pain from another area of the body as well. Referred pain is pain that starts in one part of the body but actually affects a different part of the body, so the pain you feel in your neck might be coming from somewhere else. An example of referred pain would be something like pain from the C4 & C5 joint (one of the middle joints in the neck) and send pain down through the shoulder blade.