Headache is one of the most frequently reported symptoms following traumatic brain injury (TBI). Little is known about how these headaches change over time. We describe the natural history of headache in individuals with moderate to severe TBI over 5 years after injury. A total of 316 patients were prospectively enrolled and followed at 3, 6, 12, and 60 months after injury. Individuals were 72% male, 73% white, and 55% injured in motor vehicle crashes, with an average age of 42. Pre-injury headache was reported in 17% of individuals. New or worse headache prevalence remained consistent with at least 33% at all time points. Incidence was >17% at all time points with first report of new or worse headache in 20% of participants at 60 months. Disability related to headache was high, with average headache pain (on 0-10 scale) ranging from 5.5 at baseline to 5.7 at 60 months post-injury, and reports of substantial impact on daily life across all time points. More than half of classifiable headaches matched the profile of migraine or probable migraine. Headache is a substantial problem after TBI. Results suggest that ongoing assessment and treatment of headache after TBI is needed, as this symptom may be a problem up to 5 years post-injury.