The case concerns a 12-year-old Chinese boy with Q fever, which caused inflammation of the lining of the heart (endocarditis) and subsequent kidney damage (glomerulonephritis). The boy had intermittent fever and presence of blood in the urine for 2 months, with a history of congenital heart disease (tetralogy of Fallot) and multiple heart surgeries. Diagnostic tests confirmed the presence of the bacterium Coxiella burnetii, which causes Q fever, and showed a positive PR3-ANCA antibody (109.8–158.8 CU), while other antibodies tested were negative. Cardiac ultrasound revealed significant vegetations on the pulmonary valve, and renal biopsy confirmed secondary hyperplastic glomerulonephritis. The boy was treated with doxycycline and the fever did not return; after 16 months, the hematuria disappeared, although the PR3-ANCA antibody remained positive. The case highlights the need to consider Q fever with endocarditis in children with chronic fever, hematuria, and positive ANCA, especially those with congenital heart disease.