Inadequate dietary habits in youth are known to increase the risk of onset of various diseases in adulthood. Previously, we found that female college students who skipped breakfast had higher incidences of dysmenorrhea, suggesting that breakfast skipping interferes with ovarian and uterine functions. Since dietary habits can be managed by education, it is preferable to establish a convenient screening system for meal skipping that is associated with dysmenorrhea as part of routine services of health service centers. In this study, we recruited 3172 female students aged from 18 to 25 at Kanazawa University and carried out an annual survey of the status of students’ health and lifestyle in 2019, by a questionnaire. We obtained complete responses from 3110 students and analyzed the relationship between dietary habits, such as meal skipping and history of dieting, and menstrual disorders, such as troubles or worries with menstruation, menstrual irregularity, menstrual pain, and use of oral contraceptives. The incidence of troubles or worries with menstruation was significantly higher in those with breakfast skipping (p < 0.05) and a history of dieting (p < 0.001). This survey successfully confirmed the positive relationship between breakfast skipping and menstrual pain (p < 0.001), indicating that this simple screening test is suitable for picking up breakfast skippers who are more prone to gynecologic disorders. In conclusions, since dysmenorrhea is one of the important clinical signs, breakfast skipping may become an effective marker to predict the subsequent onset of gynecological diseases at health service centers. Considering educational correction of meal skipping, breakfast skipping is a potential and preventable predictor that will contribute to managing menstrual disorders from a preventive standpoint in the future.