Chronic pulmonary thromboembolism is one of the pathogenic mechanisms for the development of pulmonary arterial hypertension in thalassemic patients, but there are no current recommendations for the management of this complication. We report performing successful pulmonary thrombo-endarterectomy in a patient with chronic thromboembolic pulmonary hypertension linked to β-thalassemia, which was followed by substantial hemodynamic and functional improvements. This report supports the feasibility of pulmonary thromboendarterectomy in thalassemic patients, and highlights the need for a comprehensive evaluation for both the presence and cause of pulmonary arterial hypertension prior to determining the likelihood of surgical cure.