On May 15, 2009, the Turkish Ministry of Health reported the first case of 2009 pandemic influenza A (H1N1) virus infection in the Republic of Turkey. Pandemic H1N1virus is a new and mutant influenza virus and has many epidemiologic and clinic features. These cases have been reported in multiple geographic regions of the world. School children are more affected than adults. In the elderly, it has a higher mortality rate. The clinical aspects of infection with H1N1 influenza A virus remains to be understood. A few cases of pulmonary embolism associated with H1N1 influenza A virus infection were reported. We herein report a pulmonary embolism in a patient with pandemic influenza A (H1N1) virus infection. A 42-year-old Turkish woman was admitted to our emergency department with dyspnea and pleuritic chest pain. She complained of fever, myalgia, sore throat and cough of four days duration on admission to our hospital. She was tested for pandemic influenza A (H1N1) virus by a polymerase chain reaction (PCR) test which revealed a positive result. Chest tomography showed pulmonary embolism. She was successfully treated with intravenous heparin and oseltamivir. This case report demonstrates the importance of considering pulmvonary embolism as a diagnosis in 2009 pandemic influenza A (H1N1) virus infected persons who present with sudden onset of dyspnea, fever and chest pain.