Background. Limited scientific evidence supports the positive effects of traditional Chinese medicine (TCM) for treating dysmenorrhea. Thus, an observation period of 3 months could verify the ancient indication that TCM treatments effectively alleviate menstrual cramps in women with primary dysmenorrhea or endometriosis. Methods. A prospective, nonrandomized study (primary dysmenorrhea and endometriosis groups) was conducted in women with dysmenorrhea for more than three consecutive menstrual cycles. All patients received TCM prescriptions based on bian zheng lun zhi theory 14 days before menstruation for a period of 12 weeks. Pain intensity was evaluated using a 10-cm visual analogue scale and two validated questionnaires (the Menstrual Distress Questionnaire and the World Health Organization Quality of Life questionnaire). Results. Of the initial 70 intent-to-treat participants, the women with dysmenorrhea reported significant alleviation of cramps during menstruation after the 12-week TCM treatment. Mixed model analysis revealed that TCM prescriptions were more effective in alleviating fatigue, hot flashes, dizziness, painful breasts, excitement, and irritability in the primary dysmenorrhea group (N = 36) than in the endometriosis group (N = 34). Conclusion. TCM prescriptions based on syndrome differentiation theory might be a potentially viable choice for treating painful menstruation and premenstrual symptoms after ruling out endometriosis.