A 16-year-old male with bone marrow failure due to chemotherapy for acute leukemia developed mitral endocarditis and a lung abscess with a bronchogastric fistula. The endocarditis was fatal despite antifungal therapy and pulmonary lobectomy with closure of the fistula followed by mitral valve replacement. Aspergillus flavus was isolated and identified at both sites. This case suggests that delayed surgical treatment and the presence of another focus of Aspergillus infection may increase the risk of death.