Venous thromboembolism may be the primary presentation in patients with polycythaemia vera (PV) and essential thrombocythemia. Most patients get diagnosed with polycythaemia vera after presenting with venous or arterial thromboembolism in the first place. Most patients tend to develop thrombosis just before or at the time of diagnosis, and this risk decreases over time. Patients aged >60 years with a history of previous thrombosis, elevated haematocrit, and leukocytosis are most at risk of thrombosis. We report a case of a 74-year-old patient presenting with shortness of breath for three days. A computerized tomography pulmonary angiogram showed bilateral pulmonary emboli with right heart strain. He underwent emergency EkoSonic™ endovascular system-directed thrombolysis (EKOS™, Boston Scientific, Marlborough, MA). The patient tested positive for the Janus kinase 2 gene mutation (JAK2), met two major and one minor criterion for PV, and was discharged home on oral anticoagulation. The Janus kinase 2 (JAK2V617F) mutation is quite common in patients with polycythaemia vera, thrombocythemia, and myelofibrosis, and these patients are at risk of both arterial and venous thrombosis, hence they require long-term follow-up.