We present the case of a 14-year-old girl who developed acute deep vein thrombosis (DVT) in her right lower extremity. Laboratory testing revealed protein S deficiency, and the patient's father also had this abnormality with a history of lower extremity DVT. Manual thromboaspiration followed by catheter-directed thrombolysis resulted in total clearance of all thrombi. Computed tomography and later venography revealed an interrupted inferior vena cava. Catheter-directed thrombolysis is an established treatment for adults with acute DVT. To the best of our knowledge, this report is the first to describe catheter-directed thrombolysis in a pediatric patient with lower extremity DVT. Our results suggest that catheter-directed thrombolysis is safe and effective for use in selected older children and adolescents with acute DVT in the lower extremity.