Hydatid cysts located in the interventricular septum are especially rare but with the high risk for intracavitary rupture. We report a patient with acute pulmonary embolism caused by an isolated, ruptured hydatid cyst on the right side of the interventricular septum. Early diagnosis was made by echocardiography and positive serology. Pulmonary artery embolism was confirmed by angiography and the patient was operated on. Embolectomy was performed by removing multiple fragments of ruptured endocyst from the left pulmonary artery, followed by surgical closure of a cyst cavity. Prompt diagnosis and an appropriate surgical treatment prevented a potentially fatal outcome.