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The bacterium <i>Coxiella burnetii</i> can cause the disease Q-fever in a wide range of animal hosts. Ruminants, including sheep, are thought to play a pivotal role in the transmission of <i>C. burnetii</i> to humans; however, the only existing livestock vaccine, namely, Coxevac^® (Ceva Animal Health Ltd., Libourne, France), a killed bacterin vaccine based on phase I <i>C. burnetii</i> strain Nine-Mile, is only approved for use in goats and cattle. In this study, a pregnant ewe challenge model was used to determine the protective effects of Coxevac^® and an experimental bacterin vaccine based on phase II <i>C. burnetii</i> against <i>C. burnetii</i> challenge. Prior to mating, ewes (<i>n</i> = 20 per group) were vaccinated subcutaneously with either Coxevac^®, the phase II vaccine, or were unvaccinated. A subset of pregnant ewes (<i>n</i> = 6) from each group was then challenged 151 days later (~100 days of gestation) with 10⁶ infectious mouse doses of <i>C. burnetii</i>, Nine-Mile strain RSA493. Both vaccines provided protection against <i>C. burnetii</i> challenge as measured by reductions in bacterial shedding in faeces, milk and vaginal mucus, and reduced abnormal pregnancies, compared to unvaccinated controls. This work highlights that the phase I vaccine Coxevac^® can protect ewes against <i>C. burnetii</i> infection. Furthermore, the phase II vaccine provided comparable levels of protection and may offer a safer and cost-effective alternative to the currently licensed vaccine.