Cryptosporidium are Apicomplexa protozoan parasites, causing diarrheal disease in man and animals, due to the lack of a licensed vaccine and resistance to the available effective therapy. This study explored the curative and the prophylactic effect of the cinnamon and ginger methanolic extracts separately and combined with nanazoxide on the experimentally infected mice with Cryptosporidium. Ninety Swiss albino mice, weight of 23-25gm, aged 7-8 weeks were divided into nine groups to assess the therapeutic and the prophylactic effect of cinnamon and ginger methanolic extracts separately then combined with nanazoxide. The result was assessed parasitologically, histopathlogically and by TEM. The best efficacy was three weeks post infection in all groups. Therapeutic effect of ginger was better than cinnamon extract, but combined ginger and nanazoxide gave the least oocyst shedding. The prophylactic dose of ginger and cinnamon methanolic extracts showed marked decrease in oocysts shedding and ginger was the best. Histopathological sections showed immune cells infiltration with a decrease in number of tissue parasite that was absent in the prophylactic groups given ginger extract. The results were confirmed by transmission electron microscopy explore a great improvement in the small intestinal brush border of the same groups.