Healthcare providers usually treat a PE in a hospital, where they can monitor your condition closely. The length of your pulmonary embolism treatment and hospital stay will vary, depending on the severity of the clot. The main treatment for a PE is an anticoagulant (blood thinner). Depending on the severity of your clot and its effect on your other organs such as your heart, you may also undergo thrombolytic therapy, surgery or interventional procedures to improve blood flow in your pulmonary arteries.