I have bronchiectasis, and there are times that I get very congested during the night. When I wake up in the early morning, I have a huge headache. I'm thinking it's because as the night hours pass, my breathing is more and more shallow, so I'm getting lower oxygen levels into my lungs, therefore not enough oxygen going to the brain.
When my lungs are clearer, I'm less likely to have a morning headache.
Beth1949