Infective endocarditis (IE) caused by microbial infection is virtually always fatal if untreated. High-dose and long-term antibiotic treatment is required to eradicate microorganisms. If increased risk of embolic events, persistent infection, and progressive cardiac failure are present, surgery is indicated. However, surgery can carry an increased risk of mortality and morbidity in critically ill children of whom other treatment options such as administering, a thrombolytic agent; recombinant tissue plasminogen activator (r-tPA) could be an alternative choice. Here, we report a 14-year-old male with Down syndrome and acute myeloblastic leukemia, diagnosed with IE characterized by two large vegetations on aortic and mitral valves, who was successfully treated with r-tPA.