Primary intravascular synovial sarcoma is a rare malignancy with only a few cases documented in the literature. On presentation, this tumour usually resembles a deep venous thrombosis (dvt) or pulmonary embolism (pe). Here, we report the case of a 20-year-old woman complaining of shortness of breath who had a history of dvt 6 weeks before presentation at our institution. Vascular ultrasound detected a suspicious mass in the right groin, which was identified as a monophasic synovial sarcoma by surgical biopsy. The tumour extended from the right superficial femoral vein into the common iliac vein, profound femoral vein, and great saphenous vein. It caused pe with near-total occlusion of the right pulmonary artery. After initial treatment on the cardiac intensive care unit, the patient was referred to the oncology department for neoadjuvant radiochemotherapy with doxorubicin-ifosfamide according to the Interdisziplinäre Arbeitsgemeinschaft Weichteilsarkome [Interdisciplinary AG Sarcomas] protocol and surgical resection of the tumour. No signs of tumour recurrence were found during the subsequent course of the disease, but the patient died from treatment complications approximately 15 months after initial presentation. This case underlines the importance of screening for malignancies even in young patients presenting with dvt or pe. We also recommend whole-leg compression ultrasonography in patients with suspected dvt or pe (as opposed to venography or simple four-point ultrasound examination in the groin and popliteal fossa) to detect possible underlying causes for thrombosis.