SARS-CoV-2 virus can produce pathogenic molecules such as ssRNA, dsRNA, spike protein can be recognized by microglial cells. However, it’s not known whether exposure to these pathogens can result in microglia-mediated neuronal damage. We aimed to investigate whether SARS-CoV-2 S1 protein and repeated treatment with mRNA vaccines can induce microglial activation and neuronal death in mixed neuronal-glial co-cultures. We treated primary rat neuronal-glial co-cultures for 3 and 7 days with SARS-CoV-2 S1 recombinant protein or mRNA Original/Omicron B.A 4-5 and Tozinameran/Riltozinameran vaccines, evaluating cell viability, microglial proliferation and cytokine secretion. SARS-CoV-2 S1 recombinant protein at concentrations 0.1-50 µg/ml had no effect on neuronal viability over 3 days incubation, whereas 50 µg/ml caused a decrease in neuronal cell numbers by 45 %. After 7 days incubation with S1 protein at 1-50 µg/ml concentrations neuronal numbers decreased by 16-29 % compared to control cultures. However, at 50 µg/ml concentration S1 significantly increased neuronal necrosis by 34 %. Repeated addition of 5 ng/ml mRNA vaccines every 24 hours for 3 days increased microglial number by 78 % compared to control cultures but had no effect on neuronal number and viability. No changes were found in cytokine TNF-alpha and IL-6 levels in media of cultures treated with S1 or vaccines. Our data show that SARS-CoV-2 S1 protein may contribute to neuronal loss in the long-term periods. Repeated application of mRNA vaccines can induce microglial proliferation though neuronal viability remains unaffected.