The aim of this study was to evaluate the perception of periodontal pain in patients treated with either fixed multibrackets or removable alignment systems with a monthly follow-up over a period of twelve months. Materials and Methods: This longitudinal clinical study comprised a sample of 140 patients (72 women; 68 men) divided into two groups of 70 patients each: the bracket group (BG) with conventional fixed brackets using the MBT technique with a 0.022″ slot and the Invisalign group (IG) with aligners (Invisalign). The visual analog scale (VAS) was used to quantify patient-reported pain. Pain analysis was conducted monthly at 4 (T1), 8 (T2), and 24 h (T3) post-follow-up as well as at 2 (T4), 3 (T5), 4 (T6), 5 (T7), 6 (T8), and 7 days (T9) post-follow-up during the first twelve months after starting orthodontic treatment. Results: Statistically significant differences (p < 0.05) were observed between both study groups in the mean pain scores on the visual analog scale (VAS) during the twelve-month follow-up period, except for during the eighth month of treatment. In the first month, the group with conventional brackets reported higher pain scores. From the second month onwards, we observed that patients with aligners described a higher level of pain compared to the group of patients with conventional brackets. In both experimental groups, though at different evaluation periods, we found that the peak of maximum pain occurred between 24 and 48 h (T3–T4) after monthly follow-up appointments; from this point, the pain decreased until reaching minimum values from the fifth day onwards (T7). Conclusions: In the first month of treatment, the patients with conventional fixed multibrackets reported the highest levels of pain compared to those with removable aligners. From the second month on, this trend changed. The patients with removable aligners reported the highest levels of pain. Therefore, the orthodontic system used influenced the perception of pain in patients.