Abstract Eimeriosis is caused by a protozoan parasite of the genus Eimeria and infection affecting most domestic animal species. The aim of this research was to comprehend the impact of selenium nanoparticles (SeNPs) on eimeriosis induced by Eimeria papillata in mouse jejunum, and how they work as antioxidants and anti-apoptotic agents against eimeriosis. The numbers of meronts, gamonts, and developing oocysts of E. papillata reduced after the infected mice were treated with the SeNPs. The levels of malondialdehyde (MDA), nitric oxide (NO), and other oxidative stress-related molecules, such as glutathione (GSH), catalase (CAT), and superoxide dismutase (SOD), were assayed. E. papillata was able to change the redox status of the jejunal cells; this was confirmed by the elevation of the MDA and NO levels, and the decrease of the GSH levels and the activities of the antioxidant enzymes CAT and SOD. SeNP treatment significantly reversed this disturbance of the redox status. The expression levels of the apoptotic markers Bax and caspase-3 in the jejunal samples were evaluated using qRT-PCR. The SeNPs decreased the Bax and caspase-3 expression after being administered to the E. papillata-infected mice. Collectively, the SeNPs demonstrated antioxidant and anti-apoptotic activities against murine eimeriosis.