Background and Objective: Repetitive transcranial magnetic stimulation (rTMS) is recommended as an effective treatment for both major depressive disorder (MDD) and treatment-resistant depression. According to the possible impact of rTMS on cognitive psychological characteristics, this study aimed to determine the effectiveness of rTMS in meta-worry and neuropsychological functions among MDD patients. Materials and Methods: This quasi-experimental study was conducted on 30 patients with MDD referring to Atieh Clinical Neuroscience Center, Tehran, Iran, in 2019. The participants were randomly divided into two groups of intervention and control (n=15 each). The data collection tools included the Beck Depression Inventory, meta-worry subscale of the Anxious Thoughts Inventory, and Cambridge Neuropsychological Test Automated Battery. Results: The comparison between the two groups showed that the scores of the meta-worry scale improved after the intervention in patients undergoing rTMS, compared to those in the control group (Z=-3.41; P=0.002); however, no difference was observed between the two groups in the follow-up (Z=-2.02; P=0.053). The assessment of neuropsychological functions among the patients undergoing rTMS and those in the control demonstrated that neuropsychological functions (i.e., Minimum Spanning Tree, Rapid Visual Information Processing, and Spatial Working Memory) were significantly different immediately after the intervention and in the follow-up (P<0.05) except for the Difficulty Maintaining Sleep (DMS) subtest. In addition, the mean depression score was significantly different between the two groups (Z=-4.17; P<0.005). There was a significant relationship between depression and all the subtests of neuropsychological functions except for DMS (P>0.05). Conclusion: In summary, the results of the current study indicated that the use of rTMS was an effective method in the improvement of neuropsychological functions except for DMS in patients with depression. However, the obtained findings did not demonstrate the persistent effect of multiple rTMS on meta-worry.