Acute Q fever is usually asymptomatic or is associated with a mild self-limited course and a favorable outcome. The occurrence of endocarditis during acute infection by Coxiella burnetii is an emerging clinical entity observed in adults that has been attributed to an autoimmune complication of early infection. Herein, we report the first case of a previously healthy 2-year-old child with endocarditis complicated by septic embolic stroke, in which the identified microbiological evidence was suggestive of acute rather than chronic C. burnetii infection. The development of endocarditis in this case occurred in the absence of any autoimmune reaction, but in the context of a very mild form of congenital heart disease, a small ventricular septal defect, which might serve as a predisposing factor for endocarditis. This case suggests that acute Q fever endocarditis may affect children as well and can be attributed not only to autoimmune mechanisms but also to a potential effect of the infectious agent per se on the cardiac endothelium in patients with underlying heart defects, regardless of their severity.