Headache is a common complaint in children, and it has a significant effect on their daily living activities. Having a definite diagnosis for the cause of the headache is very important for its appropriate management.. We report a 12-year-old boy complaining of chronic headache, with a positive family history of migraine. The only abnormal finding in his general and neurological examinations, and CT scan evaluation of his brain and paranasal sinuses, was a retention cyst in his sphenoid sinus. The child’s symptoms did not improve after receiving migraine medications or treatment for sinusitis. Further investigations revealed positive serological results for brucellosis infection. His symptoms were relieved, and imaging evidence of sinus involvement disappeared after brucellosis treatment. The child remained headache free in later follow-ups.. In evaluating the cause of children’s headaches, brucellosis must be considered in differential diagnosis..