Poor sleep patterns like sleep apnea or restless sleep can trigger a headache in the mornings. Your son could also be having âbenign intracranial hypertensionâ (BIH). This happens due to impaired CSF absorption.
A generalized throbbing headache usually feels worst in the morning and last thing at night. This headache is generally relieved on standing (consistent with raised intracranial pressure) like his improves when he gets up. It is then aggravated by straining, coughing, or a change in position, as your son suffers after 2-3 hours.
Sinusitis is another cause of morning headaches. It could also be a cluster headache, migraine, or a tension headache.
Please consult a neurologist regarding this. Hope this helps. Take care!