Background:- Major depressive disorder (MDD) is a leading cause of disability worldwide. Almost a third of patients diagnosed with MDD do not respond to antidepressants. Transcranial magnetic stimulation (TMS) is a novel option for these patients. The first approved and most frequently used protocol for TMS in patients with MDD is the 10-Hz high-frequency repetitive TMS (rTMS) over the left dorsolateral prefrontal cortex. Intermittent theta-burst stimulation (iTBS) is a recently developed FDA-approved rTMS technique with relatively short session duration (3 min) compared with the standard 10-Hz high-frequency rTMS treatment session (37.5 min). Patients and Methods:- In this double-blinded, sham-controlled trial, we recruited 51 participants aged 18–60 years, diagnosed with a current episode of treatment-resistant MDD, who were receiving stable antidepressant medication doses for at least 4 weeks before the start of sessions and had moderate to severe depression. Participants were randomly assigned 1:1:1 to treatment groups (10-Hz rTMS, iTBS, or sham). Sessions were conducted by delivering iTBS, 10-Hz rTMS, or sham parameters to the left dorsolateral prefrontal cortex as of once daily sessions (i.e. five sessions a week for at least 4 weeks, which may be extended to 6 weeks). The TMS sessions were delivered through a figure-of-eight coil connected to the Neurosoft TMS system. Primary outcome was improvement in depression, measured by changing score of Hamilton depression rating scale-17 before, each week, and after the end of sessions among the three groups, asking about adverse effects, assessed safety, and tolerability of intervention. Results:- In this RCT, the improvement in depression symptoms measured by change of Hamilton depression rating scale-17 scores between baseline score and primary end point (4 weeks) was highly statistically significant, favoring 10-Hz rTMS (14.53 points; 49.75%) over sham (5.6; 21.87%) (P<0.004). There was also a significant difference between iTBS (15.9 points; 56.68%) versus sham (5.6 points; 21.87%), with a highly significant difference in depression outcome, in favor of the active iTBS group (P=0.001). Response rates were significantly higher for 10-Hz rTMS (73.3%) and iTBS (66.7%) versus the sham (13.3%). Regarding the remission rates for the 10-Hz rTMS (20%), iTBS (40%), and sham (6.7%), the difference was statistically significant between iTBS and sham, but the 10-Hz rTMS comparison with sham has failed to show a statistically significant difference. Regarding adverse effects, there was a nonsignificant difference in reported adverse effects between different study groups. Headache was the most frequently reported adverse effect in all sample (62.2%). Conclusions:- Both conventional 10 HZ rTMS and iTBS are effective, efficacious, and tolerable for management of treatment-resistant MDD. However, iTBS is preferable than 10-HZ rTMS regarding shorter session time, which leads to increased treatment capacity.