Q fever endocarditis is the most common presentation of chronic infection of Coxiella burnetii, but it rarely occurs in the pediatric age group. We report the first case of Q fever endocarditis in an Omani child. The affected 11-year-old female lives in the Al Batinah governorate in the north of Oman and was known to have congenital heart disease. She presented with features of chronic blood culture-negative endocarditis. The C. burnetii infection was confirmed with the indirect immunofluorescence assay. The patient responded well to a combination of doxycycline and hydroxychloroquine therapy.