My mare has a cold right now. She does that I just let her cough it out. She just needs time. I'd guess your horse has a warm up cough but maybe call her vet and ask if they should come out? Are you in the open or a dirt arena?
How frequently do you run her? After a lot of exertion(if the horse doesn't work that hard regularly), it can get things running in the horses sinuses.
Your horses lungs might not be strong enough either. Do you do a lot of cardio with her?
Either way, I agree with Adeline, you should check with the vet just to be safe.