Working horses support the livelihoods of smallholder farmers in Egypt but can pose potential zoonotic risk to their handlers such as cryptosporidiosis. Working horses were recruited into the study from 37 villages/areas in two Egyptian governorates. Faecal samples were collected from 607 horses and were examined for Cryptosporidium spp. infection using modified Zielh-Neelsen staining technique. Data about signalment, concurrent disease and level of strongyle infection were collected. The prevalence of Cryptosporidium spp. infection was calculated using a bootstrap method and potential risk factors for the infection were investigated using mixed-effects logistic regression models that included the sampling location as a random-effects variable. The prevalence of Cryptosporidium spp. infection was 28.7% (95% confidence interval = 23.5–33.9). None of the variables investigated including age and sex of the animals were associated with the risk of the infection. The study identified greater prevalence of Cryptosporidium spp. infection in the study area and further studies may be required to genotype these parasites. Personal hygiene such as hand sanitation should be practiced when managing these horses.