Congenital absence of inferior vena cava (IVC) and iliac veins is a rare anomaly that can predispose young patients to develop deep vein thrombosis (DVT). This case report highlights the importance of considering this anatomical abnormality in young patients with unprovoked DVT. We present the case of a 17-year-old girl who visited the emergency department (ED) complaining of right leg pain and swelling for 8 days. An ED ultrasound revealed extensive DVT in the right leg veins, and further investigation with abdominal computed tomography revealed that the patient’s IVC and iliac veins were absent and showed the presence of thrombosis. The patient underwent thrombectomy and angioplasty by interventional radiology and was given a lifetime prescription for oral anticoagulation. When treating young, otherwise healthy individuals with unprovoked DVT, Clinicians should include absent IVC in their differential when treating young, otherwise healthy patients with unprovoked DVT.