Objective:To observe any effect of transcranial magnetic stimulation on brain activity, cognitive impairment and depression (PSCCID) after a stroke.Methods:Thirty patients with PSCCID after a stroke were randomly assigned into an observation or a control group, each of 15. For four weeks, both groups received basic medication to nourish the nerves, improve circulation, and anti-platelet, as well as 50mg/d of oral sertraline hydrochloride. Their rehabilitation involved 40 minutes of exercise daily, 30 minutes of assignment therapy and cognitive function training. The therapy was administered 5 days a week for the 4 weeks. In addition, the observation group received daily rTMS applied over the left dorsolateral prefrontal cortex at 10Hz and 100% of the motor threshold. Functional MRI was used before and after the treatment to assess the subjects′ cognition and depression, as well as any changes in the regional homogeneity (ReHo) and amplitude of low-frequency fluctuations (ALFFs) in regions of interest.Results:Significant improvement was observed in the subjects′ average Mini-mental State Examination (MMSE), Montreal Cognitive Assessment Scale (MoCA) and Hamilton Depression Scale 17-item (HAMD-17) scores, with those of the observation group significantly better than those of the control group on average. After the intervention the observation group presented several brain regions with altered ReHo and ALFF values compared with before the treatment and compared with the control group. The increases were mainly on the stimulated side while the decreases were mainly on the contralateral side. The increased ReHo in the left orbital gyrus correlated significantly with the average MMSE, MoCA and HAMD-17 scores. The increased amplitude of fluctuations in the left Heschl′s gyrus correlated significantly with the average MMSE and MoCA scores.Conclusion:rTMS can relieve depression and promote cognition after a stroke. Its effects may be associated with altered brain activity in regions related to cognitive and emotional processing.