The Coronaviridae family has again demonstrated the potential for significant neurological complications in humans during the recent pandemic. In patients, these symptoms persist throughout the infection, often lasting for months. The consequences of most of these post-infection symptoms might be linked with abnormal cytokine production and reactive oxygen species (ROS) expression, resulting in neuron damage. We investigated the effect of infection with the Mouse Hepatitis Virus (MHV) JHM strain and Sialodacryoadenitis Virus (SDAV) on a primary microglia and astrocyte culture by analysing ROS production, cytokine and chemokine expression, and cell death during one month post infection. For this purpose, confocal microscopy, flow cytometry, and a high-throughput Luminex ProcartaPlex immunopanel for 48 cytokines and chemokines were utilised. The replication of MHV-JHM and SDAV in microglia and astrocytes has increased the production of pro-inflammatory cytokines and inhibited the production of anti-inflammatory cytokines. The cytokine expression induced by the two viruses differed, as did their detection after infection. SDAV infection resulted in a much broader cytokine response compared to that of MHV-JHM. Both viruses significantly increased ROS levels and induced apoptosis in a small percentage of the cells, but without necrosis.