This study aimed to determine how common are specific red flags of life-threatening headache (LTH) among children with complaints of headache in the emergency department. A retrospective study was conducted over five years, including all patients aged < 18 years who presented for a headache to a Pediatric Emergency Department. We identified patients with life-threatening headaches and compared the recurrence of the main red flags (occipital location, vomit, nocturnal wake-up, presence of neurological signs, and family history of primary headache) to the remaining sample. Two-thousand-fifty-one children (51% female, 49% male) were included. Seven patients (0.3%) were diagnosed with a life-threatening headache. In the analysis of red flags, only the presence of abnormal neurological evaluation and vomiting was found to be more common in the LTH sample. No statistically significant difference was found for nocturnal awakening or occipital localization of pain. Urgent neuroradiological examinations were performed in 72 patients (3.5% of cases). The most common discharge diagnosis was infection-related headache (42.4%), followed by primary headaches (39.7%). This large retrospective study confirms the most recent literature suggesting that night awakenings and occipital pain are common symptoms also associated with not-LTH. Therefore, if isolated, they should not be considered red flags.