Menstruation is suggested to affect multiple sclerosis (MS) symptoms, while the effect of MS on menstruation is not studied before. Here, we aimed to compare the pattern of menstrual cycle and its symptoms between MS patients and healthy controls. This is a cross-sectional study conducted during 2015–2016 in MS clinic of Kashani hospital, Isfahan, Iran. We included female patients > 14 years with diagnosis of relapsing-remitting MS, and healthy subjects as the control group. We collected data regarding menarche age, menstrual characteristics, history of premenstrual syndrome, the amount of menstrual bleeding, and the possible perimenstrual symptoms from all subjects. Also, MS patients were asked to report changes in menstrual characteristics after MS occurrence. The final study population contained 181 MS patients and 202 healthy subjects. The mean age in MS and control group were 36.04 ± 9.86 and 35.16 ± 11.30, respectively (P-value = 0.426). Menarche age in MS patients and control group were not statistically different (13.59 ± 1.87 and 13.29 ± 1.53, respectively; P-value = 0.087). Changing menstrual characteristics was reported in 70 MS patients (38.7%). Irregular menstrual cycle increased from 21% to 40.3% after occurrence of MS (P-value < 0.001) and was reported 24.7% in the control group. MS patients versus controls reported more symptoms before, during, and after their menstrual period (P-values < 0.001). We found no difference regarding menstrual characteristics in MS patients before onset of the disease and healthy controls. Irregular menstrual cycle was observed more after the disease occurrence while other menstrual characteristics did not change. Moreover, MS patients reported many more perimenstrual symptoms.