Pulmonary embolism (PE) that occurs in patients with severe chronic obstructive pulmonary disease (COPD) can often result in acute exacerbation. Immediate intervention for them is required to prevent acute exacerbations and reduce mortality. A 72-year-old man with severe COPD developed deep vein thrombosis with PE and worsened despite anticoagulant therapy and mechanical ventilation. Thrombolysis was contraindicated due to a history of gastric bleeding 3 weeks ago. He had a pulmonary embolism severity index (PESI) score of 272, placing him in the very high-risk group, with a 30-day mortality rate of 10.0%–24.5%. Mechanical thrombectomy was performed using AngioJet® Solent catheter to remove the thrombus obstructing the right middle and lower lobe pulmonary arteries. The patient improved without complications and was discharged. PE in severe COPD requires immediate intervention due to the higher severity of symptoms compared to the general population, and the use of AngioJet ® Solent catheter may be an effectively alternative modality of treatment.