Introduction. Pure white cell aplasia (PWCA) is a rare hematologic disorder characterized by the absence of neutrophil lineages in the bone marrow, with intact megakaryopoiesis and erythropoiesis. PWCA is commonly associated with several immune pathologies. Cytopenia in patients with thymoma is a paraneoplastic syndrome, along with other manifestations. The two major clinical issues in PWCA are various infectious complications and ulcerative-necrotic lesions of the skin and mucosa membranes. Case presentation. We present a rare case of a patient with thymoma and PWCA, as paraneoplastic syndrome. On the background of agranulocytosis, the patient developed sepsis and infective endocarditis (IE) caused by a rare agent, carbapenem-resistant Klebsiella pneumoniae. Conclusions. The rarity of endocarditis caused by Klebsiella species limits its recognition and awareness of its often severe course. Most cases of endocarditis with Klebsiella pneumoniae are associated with prosthetic heart valves. In patients with immunosuppression, such as PWCA associated with thymoma, and endocarditis, rare microorganisms must be considered. © 2021 Balkan Medical Union. All rights reserved.