Introduction: Available data suggest that there is an association between endometriosis and a group of disorders including autonomic nervous system irregularities. A deeper understanding of relationship between endometriosis and autonomic nervous system is needed as it may lead to novel discoveries on the causes or consequences of endometriosis. In this study, we analyzed the prevalence of migraine in patients with endometriosis. Methods: In this cross-sectional study, medical records of women were reviewed through January 2013 to December 2017. Women with laparoscopically proven endometriosis (n = 185) were compared with those without endometriosis (n = 168). The 3-item screening questions (ID Migraine™) test was used to screen migraine. Data were analyzed using SPSS v25 (IBM Corporation). The χ² test was used for analyzing the nominal parameters and group comparisons. Pearson χ² was used to study the association between endometriosis and migraine. Results: The mean age was 31.86 ± 4.49 years of the endometriosis group and 28.95 ± 5.11 years of the controls (p = 0.408). The two pre-screening questions of ID Migraine test were answered positively by 86 patients of the endometriosis group (75.4%) and by 53 patients of the control group (54.6%) (p = 0.001). Of these patients, 51 (44.7% of endometriosis group) and 26 (26.8% of control group) were diagnosed as having migraine using 3-item Migraine questionnaire (p = 0.007). Conclusion: This study showed that the prevalence of migraine was significantly higher in patients with endometriosis. Because there is a strong correlation, patients with endometriosis should be screened for headache and migraine to increase the benefits of care.