Fenestrated Fontan operation was performed in a 19-year-old male with a diagnosis of right isomerism syndrome. Postoperatively, fungal endocarditis due to Candida Albicans and mediastinitis by Methicilin resistant Staphylococcus Aureus (MRSA) occurred. For Candida endocarditis, combined surgery and medical treatment with amphotericin B was effective. MRSA mediastinitis was successfully treated by continuous closed irrigation with 0.5% povidone-iodine solution. This is the 17th reported case of fungal endocarditis after open heart surgery in Japanese literature.