We describe the fatal course of a Candida albicans mediastinitis in a 4-year-old child after truncus arteriosus repair, leading to aortic rupture. The diagnosis was made by computer tomography and confirmed at exploratory sternotomy, with positive swab and blood cultures. After local surgical lavage, Amphotericin B therapy was started, but the child died due to aortic rupture 2 weeks later, despite negative blood cultures. The potential risk of aortic rupture with Candida mediastinitis after congenital heart repair exists, and combined aggressive surgical and medical treatment is essential. Guidelines for the diagnosis and therapy in pediatric patients with post-operative mycotic mediastinitis are required.