During the last decade, the problem of suicide has become more serious in individuals with depression. Repetitive transcranial magnetic stimulation (rTMS) is an effective treatment for major depressive disorder (MDD). This study aims to investigate the efficacy of magnetic resonance imaging (MRI)-based neuronavigation-guided daily high-dose rTMS for rapidly improving suicidal ideation in treatment-naive patients with MDD. In the present 1-week double-blind study, 42 treatment-naive patients with MDD with suicidal ideation were randomly assigned to the treatment of escitalopram oxalate tablets (10 mg/d) in combination with either active (n = 21) or sham (n = 21) rTMS. The TMS coil was positioned over a specified target location (-44, 40, and 29) in left dorsolateral prefrontal cortex based on MRI data. The severity of suicidal ideation was measured by the Beck Scale for Suicide Ideation (BSI). The 24-item Hamilton Depression Rating Scale (HAMD-24) and Montgomery-Åsberg Depression Rating Scale (MADRS) were utilized to assess the severity of depression. The Wisconsin Card Sorting Test, Continuous Performance Test, and Stroop Color-Word Test were adopted to assess executive function. In contrast to the sham group, the active rTMS group showed a significantly greater BSI score reduction at the third day and the seventh day (P < 0.001). Moreover, the active rTMS group showed a significantly greater HAMD (P < 0.001) and MADRS (P < 0.001) score reduction at the seventh day in comparison to the sham group. The present findings suggested that the neuronavigation-guided high-dose rTMS may be a novel method to rapidly reduce suicidal ideation and mitigate depressive symptoms. © 2020 The Authors Clinical Pharmacology & Therapeutics © 2020 American Society for Clinical Pharmacology and Therapeutics.