Thanks for posting your query,
From your description it is clear that your son is suffering from an infection. Fever in more than 80% of the time (especially in children) is always associated to an infection which could be viral, bacterial, parasitic, protozoa, fungi etc and most which can result to a fever and headache is a symptom that arises as a result of the infection. Headache is sometimes related to encephalitis
and that is suspected specific causes such as toxoplasmosis
that comes from cats), cryptococcosis
(fungi), viral (CMV, Adenovirus etc), malaria (i don't know if malaria is common in your environment-depends on specie of mosquitoes available in your region) and a wide variety of infections that cause encephilitis. Meningitis is unlikely given that he does not present with meningism (specific signs that help diagnose meningitis) but the present infection could complicate to meningitis. Other organ systems such as circulatory system, GIT (liver, stomach, intestines notably), urinary tract
, respiratory tract
, ENT etc could be affected as well and could cause a headache.
I suggest you consider this seriously and find him the nearest clinic or health center so that the specific cause can be found and treated. If you are far from reaching one, then provide him with analgesic pain medicines with antipyretic properties such as paracetamol, ibuprofen etc for relief of headache and control of fever. Given of broad spectrum antibiotics such as ciprofloxacin
may help cure bacteria affections (of unknown types) and also control the situation before it can get out of hand.
Hope this helps