The incidence of bacterial meningitis has decreased significantly since the development of the Hib, PCV, and meningococcal vaccines.
This means that it's important to remember there are other causes of "fever, headache, and stiff neck" in the pediatric population.
Retropharyngeal abscess will cause young children to have fever and resist moving their necks...but these children are generally non-toxic appearing.
CT with contrast of the neck will help you with your diagnosis.
It can often be treated with antibiotics only.
Acute Disseminated Encephalomeningitis (ADEM) can cause "fever, headache, and stiff neck" in addition to neurologic symptoms such as weakness, motor deficits, or seizures...the neurologic findings depend on where in the brain and/or spine demyelination occurs.
CSF will show an elevated protein count with lymphocytic predominance, and MRI will show areas of T2 hyperintensity.
It can be treated with high-dose methylprednisolone, intravenous immune globulin (IVIG), and plasmapheresis.
Rocky Mountain Spotted Fever (RMSF), despite its name, has the majority of its cases in five states NOT in the Rocky Mountains (North Carolina, Oklahoma, Arkansas, Tennessee, and Missouri).
Clinical suspicion should be high, and patients with possible RMSF should be treated with doxycycline.
Treatment is often complete before confirmatory laboratory results are available.
Blood in the brain can be very irritating and can cause children to have headache, stiff neck, and sometimes even fever.
Intracranial hemorrhage has been known to present with "fever, headache, and stiff neck," so remember to keep diagnoses such as AVM on your differential.