Cognitive impairments are a core symptom of schizophrenia. Although low-intensity repetitive transcranial magnetic stimulation (rTMS) also has cognitive improving effect like the commonly used high-intensity rTMS, it has not been applied in schizophrenia yet. To fill this gap, inpatients with schizophrenia were randomized to receive 20 sessions of daily adjunctive active low-intensity rTMS in 4 weeks, or sham treatment. At baseline, 4 weeks, and 6 months, the Positive and Negative Syndrome Scale (PANSS) was used to assess psychotic symptom severity, while the Repeatable Battery for the Assessment of Neuropsychological Status (RBANS) and the Stroop Color and Word Test (SCWT) were used to assess cognitive functions. Compared to the sixty-nine patients receiving sham treatment, those fifty-nine patients receiving active rTMS performed better in all cognitive domains at post-treatment with small to large effect sizes. This superiority of active rTMS over sham treatment remained significant at 6-month follow-up, with small to large effect sizes, except for visuospatial function and delayed memory. The reduction in PANSS scores were not correlated with cognitive improvements. Our findings provide evidence for using low-intensity rTMS to ameliorate cognitive impairments in schizophrenia. More research are needed to determine the optimal intensity for each domain of cognitive functions.