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Venous thromboembolism is a common cause of morbidity and mortality in cancer patients. Given the bleeding risks, determining treatment for malignancy-related thrombosis is challenging, especially in the case of submassive pulmonary embolism (PE) because the risk-benefit ratio in terms of bleeding risk is uncertain. Here we discuss the case of a 53-year-old man with Kartagener syndrome with situs inversus totalis and stage IV non-small cell lung cancer with a recent brain mass resection, presenting with dyspnoea and palpitations. The patient was diagnosed with a submassive PE and only underwent suction thrombectomy through the left internal jugular vein with excellent response. In conclusion, when treating submassive PE, aspiration thrombectomy without thrombolysis is preferable to thrombolysis, which may be contraindicated due to the higher risk of bleeding.