To investigate the effectiveness of moxibustion at different times of the menstrual cycle for patients with primary dysmenorrhea (PD). Participants were 208 patients allocated to three controlled groups: one pre-menstrual treatment group (Group A), one menstrual-onset treatment group (Group B), and one waiting-list group (Group C). Groups A and B received the same intervention of moxibustion on points SP6 and RN4 but at different times. Group C, the waiting-list group, received no treatment throughout the study. Cox Menstrual Symptom Scale (CMSS) score was the primary outcome. Secondary outcomes were visual analog scale (VAS) score of pain intensity, self-rating anxiety scale (SAS) score, and self-rating depression scale (SDS) score. CMSS and VAS scores were obtained at the baseline stage (three cycles), treatment stage (three cycles), and follow-up stage (three cycles), a total of seven evaluations. SAS and SDS scores were obtained on the day of group allocation and the first day of the follow-up stage, a total of two evaluations. Baseline characteristics were comparable across the three groups. Pain duration (CMSS score) was significantly higher in Group C than in the other two groups at each evaluation (P<0.001). There was also a significant difference in the improvement in pain duration between Group B and Group C (P<0.001) throughout the trial. There were no significant changes in pain severity (CMSS score) after the 3-month treatment in Group A and Group B (P>0.05). Secondary outcomes showed that pre-menstrual moxibustion (Group A) was as effective as menstrual-onset moxibustion (Group B) in relieving pain intensity (VAS score) and negative mood (SDS and SAS scores). Moxibustion appears as an effective treatment for PD. Pre-menstrual application is more effective than menstrual-onset application. ChiCTR-TRC-14004627. © 2020 Liu et al.