Objective To evaluate the gender differences in negative symptoms and cognition of schizophrenia after high-frequency repetitive transcranial magnetic stimulation（ rTMS）. Methods A total of 62 patients with chronic schizophrenia were assigned into sham rTMS group and rTMS group by random number table method. Patients in the rTMS group were stimulated with 10 Hz in the left dorsolateral prefrontal cortex（ DLPFC） for four weeks， while a special coil without actual stimulation were applied to the patients in the sham rTMS group. Positive and Negative Symptom Scale（ PANSS） was used to assess patients’ psychotic symptoms. Brief Assessment of Cognitive in Schizophrenia（ BACS） was applied to evaluate patients’ cognitive function. Results After 4-week intervention， the negative symptoms of the rTMS was significantly improved after the treatment with gender differences， thus the improvement was more evident in female after treatment （P ＜ 0.05）. The result of BACS indicated that the scores of word fluency， symbol coding， digital sequencing， token motor task， verbal memory， tower of London and category fluency in the rTMS group were all higher than those of the sham rTMS group with statistical differences（ P＜0.05）， but without gender difference（ P＞0.05）. Conclusions Application of active 10 Hz rTMS to the DLPFC can improve the negative symptoms and cognition in patients with schizophrenia. There is a gender difference in improving negative symptoms， and it shows better effect in female.