Objectives: The treatment of Burning Mouth Syndrome (BMS) represents a challenge in tailoring appropriate medication for individual patients. The augmentation of pregabalin to conventional treatment has shown promising outcomes in relieving pain and improving the quality of life in chronic pain conditions. This study aimed to compare the efficacy of vortioxetine with other antidepressants (SSRIs/SNRIs) in combination with pregabalin in a cohort of unresponsive BMS patients and to predict treatment response by using clinical data. Methods: A 52-week randomized, open-label, comparative clinical study was conducted, enrolling 203 BMS patients previously treated with one antidepressant for 12 weeks and non-responders to the treatment (clinical trial registration: NCT06025474). The study sample included two groups: Group A (136) received vortioxetine, while Group B (67) received SSRIs/SNRIs. Pregabalin (75 mg/day) was added to both groups, with a potential dosage increase to 150 mg/day for inadequate responders after 12 weeks. Treatment response was assessed with VAS and SF-MPQ, HAM-A, and HAM-D scores at 12, 24, 36, and 52 weeks. Stepwise logistic regression analysis was used to predict treatment response. Results: A total of 84 (61.8%) BMS patients in Group A and 39 (58.2%) in Group B showed treatment response. Group A reported a faster onset of action compared to Group B (44.8% versus 22.4% at time 1; p:0.002**) and lower adverse event rates (8.8% versus 20.8%; p:0.001). Conclusion: The addition of pregabalin to vortioxetine may be considered a potential treatment option for BMS. Further research is required to corroborate these findings and optimize personalized treatment approaches for BMS patients.