Although antipsychotic medications are effective in managing schizophrenia (SCZ), there are still no effective strategies or preventive measures to address the weight gain associated with the long-term use of these medications. We performed a single-blind, randomized, sham-controlled clinical trial to explore the efficacy of noninvasive high-frequency repetitive transcranial magnetic stimulation (rTMS) technology in reducing body weight in patients with SCZ. Fifty-three obese patients with chronic stable SCZ (BMI ≥30 kg/m) completed a 4-week intervention study. The primary outcomes were the changes in body weight and body mass index (BMI) before and after the rTMS intervention. Secondary outcomes included changes in psychiatric symptoms, cognitive function, and routine blood indicators before and after the rTMS intervention. Significant changes in weight and BMI were found before and after the rTMS intervention in the active stimulation group (mean change = -2.25 kg, P < 0.01; mean change = -0.08, P < 0.001). Weight and BMI decreased significantly more in the active stimulation group compared to the sham stimulation group 4 weeks after the intervention (all P < 0.05). In the active stimulation group, immediate memory, attention, and delayed memory were significantly elevated before and after the rTMS intervention (P < 0.001). Delayed memory was more significantly elevated in the active stimulation group relative to the sham stimulation group 4 weeks after the intervention (P < 0.05). In the active stimulation group, weight change was significantly correlated with attention change and cognitive total score change (all P < 0.05). In the active stimulation group, BMI change was significantly associated with attention change and cognitive total score change (all P < 0.05). Our findings indicate that high-frequency rTMS could serve as a potential method for reducing body weight in obese patients with chronic stable SCZ.