Hi,
How is your son? Are there other symptoms present? Fever with headache and neck pain warrants further evaluation by your doctor. It is best that you have him checked for proper diagnosis. Meningitis or inflammation of the thin tissue that surrounds the brain and spinal cord and may present with sudden fever, severe headache and stiff neck. This requires immediate attention because it can lead to serious complications. Take care and do keep us posted.
Take him to your family MD. These days you can't be too safe. Bad headaces often go with the flu, BUT also go with meningitis. IF he was my son, he'd be in the doctor's office.