Continuous prostanoid infusion is an established treatment for pulmonary arterial hypertension that has led to improvements in symptoms, exercise tolerance, and survival. Patients with pulmonary arterial hypertension (PAH) who develop sepsis frequently experience clinical and hemodynamic deterioration associated with poor outcomes. Successful management of sepsis involves identification of the source of infection, early antimicrobial administration, judicious fluid resuscitation, and continuation of specific PAH therapies. We describe successful management of a patient with idiopathic PAH receiving chronic intravenous prostacyclin therapy who developed an aortic root abscess due to Clostridium perfringens requiring emergent aortic root repair. Management involved imaging studies, removal of potential sources with administration of intravenous antibiotics, and cautious fluid administration with hemodynamic monitoring. A multidisciplinary group led by a PAH specialist worked cohesively before, during, and after surgical intervention and achieved a successful outcome.