Background and objective: The aim of this prospective, single-center, controlled clinical trial was to evaluate the effects of menstrual cycle phases on orthodontic pain perception. Materials and methods: A total of 48 women between 16 and 20 years old with regular menstrual periods who were scheduled to undergo extraction of two upper first premolars for orthodontic treatment were enrolled in this study. Laceback ligatures were used to move canines distally. After activating the laceback ligatures, each patient completed a questionnaire in order to assess pain and quality of life. Pain perception was recorded by patients on a visual analogue scale (VAS) and a verbal rating scale-4 (VRS) immediately after activation (T1) and 24 h after activation (T2). During the appointment, each patient’s menstrual-cycle phase (follicular or luteal) was determined by asking some questions about her cycle. For statistical analysis of data, the Mann–Whitney U, independent t test, and Wilcoxon tests were applied. Results: Mean orthodontic pain score was 1.96 ± 0.80 and 47.08 ± 21.68 in the follicular phase, 1.92 ± 0.82 and 46.25 ± 18.92 in the luteal phase at T1 using the VRS and VAS, respectively. Orthodontic pain scores were worse in those patients in the luteal phase than those in the follicular phase (p < 0.05) in terms of both VRS (p = 0.025) and VAS (p = 0.046). No significant difference between pain scores at T1 and those at T2 in both luteal and follicular phases (p > 0.05) were observed. Conclusion: The menstrual phase has an influence on the perception of orthodontic pain which is higher in the luteal phase following the activation of laceback ligatures. In clinical practice, the phases of the menstrual cycle may have a significant role in how women perceive orthodontic pain.