The purposes of this research were to study the restoration on the cognitive ability of rat models with vascular dementia (VaD) by repetitive transcranial magnetic stimulation (rTMS) treatment and its impacts on synaptic plasticity in hippocampal CA1 area and to further explore the molecular mechanisms of the rTMS treatment on vascular dementia. Thirty-six male Wistar rats were randomly divided into four groups: the normal control group, the vascular dementia model group, the low-frequency rTMS group, and the high-frequency rTMS group. Two-vessel occlusion was employed to make VaD models. Low-frequency rTMS group rats were treated with 0.5 Hz rTMS for 6 weeks. High-frequency rTMS group rats underwent 5 Hz rTMS for 6 weeks. Morris water maze was carried out to detect the ability of spatial learning and memory of rats. The ultra-structural changes of synapses in four groups were observed by transmission electron microscope. Then the expressions of brain-derived neurotrophic factor (BDNF), NMDAR1, and Synaptophysin (SYN) mRNA and proteins in hippocampal CA1 area were determined by real-time PCR, western blot, and immunohistochemistry assay. After rTMS treatment, the learning and memory abilities of VaD rats improved significantly. The ultra-structures of synapses in hippocampal CA1 area in rTMS groups were reformed. The mRNA and protein expressions of BDNF, NMDAR1, and SYN in the low-frequency rTMS group and in the high-frequency rTMS group were higher than that in VaD model group (P < 0.05). rTMS plays an important and beneficial role in the restoration treatment of vascular dementia, which may be related to the mechanism that rTMS can increase the mRNA and protein expressions of BDNF, NMDAR1, and SYN and affect the synaptic plasticity in hippocampal CA1 area.