Chronic thromboembolic pulmonary hypertension (CTEPH) can be treated with pulmonary thromboendarterectomy (PTE) which may lead to reperfusion lung injury (RPLI) and postoperative pneumonia. We aimed to describe the incidence, diagnostic characteristics, and clinical outcomes of post-PTE pneumonia compared to RPLI. A retrospective study involving CTEPH subjects who underwent PTE at a large referral center was conducted. Data included demographics, hemodynamics, microbiologic diagnostics, and clinical outcomes. Post-PTE pneumonia was diagnosed based on documentation, signs/symptoms, or microbiologic sampling within seven days of surgery. Among 75 PTE subjects, 21 (28%) had RPLI, and 18 (24%) had post-PTE pneumonia. Of those with RPLI, 48% had pneumonia, suggesting overlap. Eight of 75 (11%) subjects underwent bronchoscopic sampling, and five (63%) samples yielded positive results indicative of infection. Subjects with post-PTE pneumonia and RPLI had longer hospital and ICU lengths of stay and mechanical ventilation duration than either group alone. Post-PTE pneumonia is prevalent and overlaps with RPLI in CTEPH subjects. The study highlights the importance of systematic evaluation and early detection of pneumonia in subjects with RPLI post-PTE. Timely diagnosis and management of pneumonia may improve outcomes. Further research is needed to understand risk factors and develop preventive strategies for post-PTE pneumonia.