Q fever is a worldwide zoonotic infection caused by Coxiella burnetii. In Belgium, the disease must be notified, and the incidence is low. Human contamination is mostly due to sheep and goats. Herein, we report a case of chronic Q fever presenting as a prolonged fever in a patient with a history of valve prosthesis. Blood culture-negative endocarditis was diagnosed through an assessment including echocardiography and systematic serological testing. Despite the absence of travel abroad or obvious contact with domestic or wildlife animals, C. burnetii phase I and phase II IgG antibody titers were > 1:8192, and polymerase chain reaction performed on blood was positive for C. burnetii. Genotypic single nucleotide polymorphism (SNP) analysis of the pathogen strain identified a SNP-type 1 genomic group, which is associated with small ruminants in Belgium. The epidemiological investigation did not confirm the presence of positive C. burnetii cattle or sheep herds in the vicinity of the patient’s workplace and home, nor in the pest animals surrounding the workplace. Patients with risk factors for chronic Q fever should be tested for C. burnetii infection in case of prolonged fever of unknown origin, osteomyelitis, abscess or blood culture-negative endocarditis, even in the absence of direct exposure to animals.