The relationship of chronic daily headache (CDH) and childhood adversity is still controversial. We therefore conducted a survey for CDH (≥15 days/month, average ≥ 2 h/day) among all students in three public schools in Taiwan. The Global Family Environment Scale (GFES), which yields a score according to childhood adverse events in the family, was used to compare childhood adversity between cases of CDH and their age- and sex-matched controls. In total, 4645 students were surveyed and 58 with CDH were identified. Significantly lower GFES scores, indicative of worse childhood adversities, were evident in the CDH group (76.7 ± 19.2), compared with the control group (86.0 ± 8.9, P = 0.001). Physical abuse (10% vs. 0, P = 0.012) and parental divorce (17% vs. 3%, odds ratio = 5.8, P = 0.015) were more frequent in the CDH group. The results indicate that childhood adversitys may contribute to greater risk of the development of CDH in young adolescents.