To determine the prevalence and experience of migraines in adolescents with surgically confirmed endometriosis compared with those without endometriosis. Cross-sectional study conducted within The Women's Health Study: From Adolescence to Adulthood-an ongoing longitudinal cohort. Boston Center for Endometriosis. Adolescent females enrolled November 2012 through November 2016. The case group included adolescents surgically diagnosed with endometriosis. The control group included adolescents without endometriosis, recruited from the local community and clinics. Not available. An extensive online health questionnaire regarding medical history, lifestyle, medication use, anthropometrics, and symptom experience and treatments. Migraine diagnosis was self-reported. Migraine pain and noncyclic pelvic pain severity were rated using an 11-point numerical rating scale. Cyclic pelvic pain was categorized. Adolescents with endometriosis were more likely to experience migraines (69.3%) than those without endometriosis (30.7%) (multivariable odds ratio = 4.77, 95% confidence interval 2.53, 9.02). For each 1-point increase in the migraine numerical rating scale, the odds of endometriosis increased by 22% (multivariable odds ratio = 1.22, 95% confidence interval 1.03, 1.44; Ptrend = .02). Among those with endometriosis, age of menarche was associated inversely with the odds of migraines. Participants with endometriosis and migraines have more dysmenorrhea than those without migraines. Adolescents with endometriosis are more likely to experience migraines than adolescents without endometriosis. A linear relationship exists between migraine pain severity and the odds of endometriosis, suggesting heightened pain sensitivity for adolescents with endometriosis. Due to the strong correlation, patients who present with either condition should be screened for comorbidity to maximize the benefits of care.