Hydatidosis is a serious parasitic infection in endemic areas. A rare presentation is pulmonary arterial cysts causing thromboembolic pulmonary hypertension. We report the case of a young man who presented with clinical and radiological findings of thromboembolic pulmonary hypertension. The patient was found to have hydatid cysts in both pulmonary arteries and in the right ventricular outflow tract. To remove all cysts without causing rupture, anaphylactic shock or systemic emboli, placing the patient under cardiopulmonary arrest was necessary, and in the case of pulmonary arterial involvement, total circulatory arrest was necessary. The cysts were removed successfully, and the patient survived the operation. The patient is being followed up on albendazole treatment. Myocardial preservation and management of total circulatory arrest are the cornerstones of a successful surgical outcome.