Background The ductus arteriosus, an essential fetal structure, normally closes spontaneously soon after birth. It’s persistence into late adulthood is considered rare; infective endarteritis complicating a patent ductus arteriosus (PDA) is an even rarer event. The clinical picture of an infected PDA could be subtle, and the diagnosis is frequently delayed. Case presentation We present the case of a young women who presented with prolonged fever, in whom we made the diagnosis of a patent ductus arteriosus complicated by infective endarteritis with vegetations in both pulmonary and aortic wall with mycotic aneurysms of the descending aorta. She underwent surgery and postoperative course was uneventful. Conclusion To our knowledge, this is the first reported case of a patent ductus arteriosus complicated with both pulmonary and aortic endarteritis.