This study aims to explore the efficacy of a new repetitive transcranial magnetic stimulation (rTMS) treatment protocol for primary trigeminal neuralgia (PTN). Methods: Sixty-four patients with PTN were randomly divided into a control group and a treatment group, each consisting of 32 patients. The control group received standard carbamazepine treatment, while the treatment group was given a progressive decremental rTMS therapy (5 sessions per week for weeks 1-2; 2 sessions per week for weeks 3-4; 1 session per week for weeks 5-8) in addition to carbamazepine treatment. Both groups underwent an 8-week treatment period. The enrollment time point was designated as T0, and at the end of each week (T1-T8), assessments were recorded. Visual Analogue Scale (VAS) and Brief Pain Inventory (BPI) were used to evaluate pain-related indicators at T0-T8. Pittsburgh Sleep Quality Index (PSQI) was used to assess sleep quality at T0, T4, and T8, and the BPI item assessing the impact of pain on daily life was used to evaluate quality of life. Results: Two patients dropped out from each group, resulting in a final inclusion of 30 patients per group. There were no statistically significant differences in VAS and BPI pain severity scores between the two groups at T0 and T1 (P> 0.05). From T2 to T8, the VAS and BPI pain severity scores decreased significantly more in the treatment group compared to the control group (P<0.05). Before treatment, there were no statistically significant differences in the scores of the impact of pain on daily life and PSQI between the two groups (P>0.05). At T4 and T8, the treatment group showed a significantly greater reduction in the impact of pain on daily life and PSQI scores compared to the control group (P<0.05). Conclusion: The rTMS treatment protocol adopted in this study can effectively alleviate pain in PTN patients, reduce the impact of pain on daily living functions, and improve sleep quality.