Headache is one of the most common presentations to the paediatric emergency department. Although challenging, it is important to differentiate serious secondary headaches requiring emergency treatment from primary headache disorders. A detailed history and neurological examination can be used to identify children at higher risk of serious underlying pathology. Neuroimaging decisions should be taken carefully, weighing risk versus benefit in each case. This article will discuss five patient scenarios highlighting red flags and differential diagnoses in children presenting with headache in the emergency department.