Post-stroke epilepsy (PSE) has a negative effect on stroke prognosis and quality of life. The CD40/CD40L system is reported to be involved in the progression of multiple disease states. We investigated the association between functional polymorphism of CD40 and PSE susceptibility, and we also explored the role of the CD40/CD40L system in PSE. A case-control study was performed in 410 ischemic stroke (IS) patients and in 389 PSE patients. Genotyping was performed by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). The CD40 mRNA and protein levels were determined by real-time PCR and western blotting, respectively. The plasma sCD40L level was detected using an ELISA kit. The frequency of the T allele in PSE patients was significantly higher than in IS patients (P<0.05). The plasma sCD40L level was significantly higher in the PSE patients than in the healthy controls and IS patients (P<0.01, P<0.05, respectively). The peripheral blood mononuclear cells (PBMCs) from PSE patients showed significantly higher CD40 mRNA and protein expression than the healthy controls and IS patients (P<0.01, P<0.05, respectively). In the PSE patients, the T-allele carriers showed increased plasma sCD40L levels and increased CD40 mRNA expression. Our study suggested that the T allele of the CD40 -1C/T polymorphism may be associated with PSE susceptibility. The CD40/CD40L system is involved in the process of PSE.