I read your question and I understand your query. Many types of infection can cause headache and fever, it s hard to be precise without knowing more about physical exam and history. The most probable cause in your case, assuming that they didn t find anything specific in their physical exam would be influenza given it s high frequency and the negative test results. If that is the case simple supportive treatment is needed, take a lot of fluids, vitamin C, over the counter medication for fever and pain like acetaminophen or ibuprofen. If you have some new symptoms or the situations persists for many days you should be checked up again. I wish you a speedy recovery.