A 8-year-old boy developed mediastinitis after direct closure of atrial septal defect. Methicillin-resistant Staphylococcus aureus (MRSA) was detected from the wound. Intermittent wound irrigation with povidone-iodine solution and vancomycin solution was protracted for two months. After the remission of MRSA infection, implantation of pectoralis major muscle flap was performed. Without recurrence of infection the wound was healed completely. Although pectoralis major muscle flap is an effective method of choice for mediastinitis, an appropriate timing of enforcing this method should be investigated hereafter.