We herein report two cases of septic pulmonary embolism that developed in patients with atopic dermatitis. The first case involved a 42-year-old man with untreated atopic dermatitis who suffered from influenza and asthma; various drugs were administered to the patient via a peripheral intravenous line. Ten days after admission, he developed septic phlebitis where the intravenous line had been inserted, a methicillin-resistant Staphylococcus aureus (MRSA) blood stream infection and septic pulmonary embolism. The second case involved a 33-year-old man with atopic dermatitis who had defaulted from his treatment. He developed infectious endocarditis and septic pulmonary embolism after receiving acupuncture. Including our cases, six cases of septic pulmonary embolism have been reported in patients with atopic dermatitis. Patients with atopic dermatitis may easily develop septic pulmonary embolism as a result of S. aureus after undergoing minimally invasive procedures, such as the insertion of a peripheral intravenous line or acupuncture. Further cases should be collected.