Objectiye To study the mechanism by which transcranial magnetic stimulation (rTMS) affects cognitive dysfunction in vascular dementia (VD). Methods Thirty-six male Wistar rats were randomly divided into a control group, a VD group, a low frequency rTMS group and a high frequency rTMS group. Two-vessel occlusion was employed to induce VD models. Low frequency rTMS group rats were given 0.5 Hz rTMS for six weeks. High frequency rTMS group rats were given 5 Hz rTMS for six weeks. Morris' water maze test was used to measure their spatial learning ability and memory. The ultrastructures of the synapses in the four groups were detected with transmission electron microscopy. The expression of synaptophysin (SYN), brain derived neurotrophic factor (BDNF) and Nmethyl-D-aspartate receptor 1 ( NMDAR1 ) mRNA and protein in the hippocampus were determined by real-time PCR and Western blotting. Results The behavior and morphology of the rats treated with rTMS improved. The average expression of SYN, BDNF and NMDAR1 mRNA and protein in the low frequency rTMS group and the high frequency rTMS group were significantly higher than in the VD group. Conclusion rTMS can provide a rehabilitative effect for VD. The mechanism might be associated with enhancing the expression of SYN, BDNF and NMDAR1 in the hippocampus.