A headache should not occur after a running session. If the individual experiences an episode after physical activity, the doctor should be consulted to know what is happening so that diagnostic tests are performed and rule out other conditions. Always bear in mind that mild exertion as well as straining, sneezing, lifting, bending or running should not trigger a headache.
Benign exertional headache
Even though exercise typically helps ease the pain, if the individual experiences a severe headache after running, a doctor should be consulted. The doctor might diagnose the individual with benign exertional headache that is triggered by sneezing or a strenuous run. If the individual develops this condition, there might be pain for only a few months or for several hours. Once the individual suffers from migraine headaches, exercise should be avoided during a migraine attack.

Neurological issues
Abnormalities inside the brain can instigate a severe exertional headache. Once the doctor is aware about his/her symptoms, MRI might be required. If the individual has a genetic predisposition to migraine headaches, he/she is likely to suffer from exertional headaches.
The doctor will also check the blood pressure and perform thyroid screen test. If subarachnoid hemorrhage is suspected, lumbar puncture might be performed.
Important considerations to bear in mind
If the individual develops severe headaches during or after a run or any physical activity, the doctor will rule out an obstructive lesion in the lower aorta. Other health conditions should be considered and ruled out such as tumors, arteriovenous malformation and subarachnoid hemorrhage from an aneurysm, chronic subdural hematoma as well as colloid cyst of the third ventricle, hypoglycemia, meningitis, stroke or chronic obstructive pulmonary disease.
Treatment for headache
Anti-inflammatory medications such as indomethacin or naproxen can be taken 1-2 hours before an exercise routine to prevent headaches. The typical dosage is 500mg for naproxen while 50-75mg for indomethacin. Other medications that can be used include ibuprofen, aspirin or ergotamine.
In case the individual experiences a severe headache after running, the treatment for migraine headaches or severe muscle contractions can be beneficial. These measures include the application of a cold compress, medications and resting in a quiet dark room. There are also over-the-counter pain medications that contain caffeine that can also help or the doctor will prescribe medication to manage the migraines.