Cystic echinococcosis (CE) is a zoonotic disease caused by the larval stage of Echinococcus granulosus species (sensu lato, s.l.). In East Africa, several species/strains occur in livestock, wildlife, and humans, but there is limited information on frequencies of infection by different genotypes in the various mammalian hosts. We have obtained data on E. granulosus infection prevalence in sheep sampled from abattoirs in Narok County, southern Kenya. We inspected carcasses for the presence of hydatid cysts in 180 sheep randomly selected in five sub-locations. The overall prevalence was 16.0% (144/900 animals), with the majority of cysts (50.7%) found in the liver, followed by the lungs (36.8%), while infections involving the liver and lungs were detected in 12.5% of the sheep. PCR–RFLP genotyping of the mitochondrial nad-1 gene in all the 343 cysts identified E. granulosus G1–G3 (sensu stricto, s.s.) as the only genotype. The majority of the cysts (62.1%) were fertile, and 35.2% were sterile, while 2.7% were calcified. Considering cyst fertility, 73.02% of lung cysts were fertile compared to 53.4% in liver cysts. Our data extends previous CE studies in livestock and indicates a high level of CE infection of sheep in Narok, with a predominance of E. granulosus s.s., which is highly pathogenic and commonly infects humans. Given the high fertility rates observed in the cysts, there is an urgent need to determine whether there is a significant incidence of human infection in Narok, and initiate “One Health” control measures.