To improve estimates of C. burnetii epidemiology in Kenya, a survey was undertaken in small ruminants in Baringo County, where acute cases of Q fever in humans had been reported in 2014. From 140 household herds selected, 508 (60.5%) goats and 332 (39.5%) sheep were included and an indirect ELISA assay for C. burnetii IgG antibodies performed. In addition, epidemiological information at both herd and animal level was collected. Generalized mixed‐effects multivariable logistic model using herd as the random effect was used to determine variables correlated to the outcome. Overall seroprevalence was 20.5% (95% CI: 17.8%, 23.3%). Goats had 26.0% (95% CI: 22.2%, 30.0%) compared to sheep 12.2% (95% CI: 8.7%, 16.0%). Nomadic pastoralism, goats and older animals (>1 year) were associated with greater risk of C. burnetii seropositivity (P = ≤0.05). Heterogeneity in C. burnetii seropositivity was observed across the sublocations (P = 0.028). Evidence of C. burnetii exposure in small ruminants revealed poses a potential risk of exposure to the people living in close proximity to the animals. We recommended integrated animal–human surveillance and socio‐economic studies for C. burnetii, to aid our understanding of the risk of transmission between the animals and humans, and in the design of prevention and control strategies for the disease in the region.