Massive pulmonary embolism (PE) in a small child is a rare event and unified guidelines for its treatment are missing. Timely diagnosis and management of massive pulmonary embolism is of crucial importance for a good outcome. We describe a unique management of PE causing oxygenation failure using a combination of catheter extraction technique, and regional thrombolysis on top of systemic heparin administration and inferior vena cava filter placement. Pulmonary hypertension was treated with inhaled nitric oxide. We believe that catheter extraction technique and regional thrombolysis is an option to consider provided that resources and expertise are available. Preoperative placement of an inferior vena cava filter should be contemplated in such high risk situations.