We report a 32-year-old man with herpes simplex virus encephalitis who developed massive pulmonary thromboembolism with mobile right atrial thrombi during treatment for this condition. It was not safe to use thrombolytic therapy because of the high risk of cerebral bleeding associated with encephalitis. The patient was initially treated at another center, but his condition deteriorated during nadroparin therapy and he was referred to our hospital. Nadroparin was discontinued, and a continuous infusion of unfractionated heparin was administered through a central venous catheter.