We report a rare case of pulmonary prosthetic valve endocarditis due to Aspergillus fumigatus, associated with septic pulmonary embolism and secondary pulmonary hypertension, in a 4-year-old boy with surgically corrected tetralogy of Fallot. The diagnosis and treatment of Aspergillus endocarditis remains highly challenging. The best therapeutic option for chronic thromboembolic pulmonary hypertension due to an infectious thromboembolic event is highly debatable and the results are poor.