The accumulation of aggregated forms of the α-Synuclein (α-Syn) is associated with the pathogenesis of Parkinson's disease (PD), a chronic progressive neurodegenerative disorder. Extensive evidences have shown the promising effects of Ginkgo biloba consumption on motor activity after PD. However, the mechanisms underline the α-Syn-induced cell damage and whether ginkgolides exert neuroprotection against this injury are unclear. Here we showed that aggregated recombinant human α-Syn, but not α-Syn monomers, triggered cell injury in cultured human neuroblastoma cell line SH-SY5Y in an apoptosis way by using flow cytometry and western blot assay. Moreover, pre-treatment with the Ginkgolide B (GB) or Bilobalide (BB) protected SH-SY5Y cells against α-Syn-induced cell viability decreases, and reduced cell apoptosis after aggregated α-Syn stimulation. Together, we firstly find that aggregated α-Syn induced cell apoptosis and GB and BB may attenuate aggregated α-Syn-induced cell apoptosis, which gives us an insight into the novel therapy for PD in future.