Few studies have discussed the development of post-traumatic headache (PTH) after zygoma fracture. This research aimed to examine the association between zygoma fracture and PTH and its other associated factors. A total of 3043 patients with zygoma fracture and 3043 patients with non-fracture were included in this analysis. They were matched to a non-fracture cohort from the National Health Insurance database according to age, sex, and index year. The incidence of PTH and its association with zygoma fracture were assessed. The zygoma fracture cohort had a significantly higher cumulative incidence of PTH than the non-fracture cohort in a 10-year follow-up. The confounding risk factors of PTH included zygoma fracture, female sex, and comorbidities, including obesity and depression. Female patients under 40 years old who had zygoma fractures had a higher incidence of PTH than the non-fracture group. Moreover, patients with zygoma fractures commonly developed PTH within three months after injury. Female patients under 40 years old with precedent zygoma fractures had a higher incidence rate of PTH than those without fractures. Moreover, patients with zygoma fractures commonly developed PTH within three months after injury. Nevertheless, before widely applying our results, a prospective study must be conducted to verify the risk factors found in this study.