Aim The present study aims to assess the anxiety in endometriosis women. Background Endometriosis is a disease with chronic pain due to the presence of endometrial-like tissue in other organs of the body. Pain and infertility can reduce the quality of mental health in women’s underlying endometriosis. Objectives The present study wants to assess anxiety in endometriosis women and compare it with healthy women in Arak City in 2023. Methods The current research was conducted using a cross-sectional method. Eighty-four records of women who were diagnosed and treated by laparoscopy in one of the referral hospitals were included. In the control group, women who were referred to health centers for an annual checkup without any history of endometriosis were recruited for the study. They were entered into the study by convenience sampling. Two groups filled out the demographic and Anxiety Beck Inventory in 15 minutes. Data was analyzed through descriptive and inferential statistics using chi-square and t-tests using STATA software. Results The results showed that the mean age of patients in the case and control groups was 31.5 ±5.7 and 31.1 ±6.1, respectively (p=0.57). Findings revealed that there was a statistically significant difference in the mean scores of FSFI between the case and control, respectively (23.08 ±6.1vs 24.47 ±6.6; p=0.031). Conclusion The present study showed that women with endometriosis still experience more anxiety after surgery than healthy women. Therefore, the reasons for women's anxiety should be identified during consultations, and drug and non-drug treatment methods should be used to reduce their anxiety.