Defects in the skin's barrier function are known to make it more likely for skin and soft tissue infection to occur in association with atopic dermatitis. These secondary infections sometimes develop into systemic infections such as bacteremia. Here, we report on our use of anti-IL-4/13 monoclonal antibody (dupilumab) on two cases with atopic dermatitis that was refractory to conventional management techniques and who had a history of serious infection (bacteremia and associated sternal osteomyelitis, infective endocarditis) caused by Staphylococcus aureus. Both cases had underlying congenital heart disease. The dermatological symptoms of both cases showed marked improvement at 16 weeks after the start of dupilumab use. The use of dupilumab on atopic dermatitis may lead to less risk of infection of skin and soft tissues deveroping serious infections due to an underlying congenital disease. When determining the treatment strategy, the cooperation of specialists in a variety of fields as well as the primary care physician was important.