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Deep transcranial magnetic stimulation (DTMS) is a noninvasive therapy for treatment-resistant major depressive disorder (MDD). The current study aimed to update a previous meta-analysis by investigating the acute and longer-term clinical outcomes of DTMS and their possible predictors (patient characteristics and stimulation parameters) in unipolar MDD. A systematic literature search identified 11 studies with 282 treatment-resistant, unipolar MDD patients. The clinical outcomes (depression severity, response and remission rates) were evaluated using random-effects meta-analyses. High frequency and intensity DTMS protocol with H1-coil had significant acute antidepressant outcomes and improved some cognitive functions after 20 daily sessions in unipolar MDD. Response rates tended to increase with lower severity of illness. Antidepressant effects were prolonged if maintenance DTMS was used after daily stimulation phases. DTMS consistently improves various symptom domains (antidepressant, cognitive) in treatment-resistant unipolar MDD.