Could a two week headache be eencephalitis? if it was caused from the flu shot would it last this long or be getting worse?

Possibly...unlikely: The statement that you have anxiety provided a clue to your headaches. Flu shots do not cause illnesses even though they have been frequently accused. See a doctor to see can be done for your headache. Remember that teeth-grinding often causes bad headaches.

Encephalitis: Encephalitis in your case is not likely as it causes fever, confusion, drowsiness and often coma. Your headaches could be due to sinusitis, or tension. Reaction to the flu shot wouldn't last 2 weeks. If the headaches worsen or persist, see your pcp for evaluation.

Only if severe: If this is a totally different type of headache from those you may have ever had, it might possibly be from a viral infection. Technically such an infection could be viral meningitis, but this is very different from the fatal cases of bacterial meningitis that you may have heard of. Viral encephalitis tends to cause a more severe illness which, in your case, would have required hospital care.

Maybe not: I would expect you to be very sick and have more problems than headache with encephalitis. I'd talk to your doctor soon and address your concern.