© 2022 College of Physicians and Surgeons Pakistan. All rights reserved.Objective: To determine relationship between the therapeutic effect of repetitive transcranial magnetic stimulation (rTMS) on cognitive impairment and brain derived neurotrophic factor (BDNF), glial cell derived neurotrophic factor (GDNF) levels in treatment resistant depression (TRD). Study Design: Descriptive study. Place and Duration of Study: Psychiatry Clinic of Konya Beyhekim Training and Research Hospital in Turkey, between June and November 2019. Methodology: The study included 33 TRD patients and 33 healthy subjects. Patients received a total of 20 sessions of rTMS treatment. Serum BDNF and GDNF levels were measured before and after rTMS treatment. Additionally, the severity of depression as well as cognitive functions were assessed at the baseline and after the treatment. Results: The rTMS treatment significantly improved depressive and cognitive symptoms in patients with TRD. Although the level of serum BDNF and GDNF increased after rTMS treatment, it was associated with the improvement in symptoms, but not significantly. Conclusions: rTMS treatment contributes to the antidepressant effect by normalising serum BDNF and GDNF levels in patients with TRD. Adding rTMS to antidepressants is, therefore, an appropriate treatment option for depressive patients with cognitive impairment.