Background Aspergillus endocarditis (AE) is a rare fatal infection. The infection is often reported in patients with prosthetic heart valves, immunosuppressed, broad‐spectrum antimicrobial use regimens, and drug abusers. Methods Herein, we report a rare case of native mitral valve AE in a 63‐year‐old man, with a probable COVID‐19‐associated invasive pulmonary aspergillosis nine months ago treated with antifungals. Results In the last admission, the lethargy, neurological deficit, and septic‐embolic brain abscess in brain MRI led to suspicion of infective endocarditis. Transesophageal two‐dimensional echocardiography and color Doppler flow velocity mapping showed a large highly mobile mass destroying leaflet and severe mitral regurgitation. The Surgical valve replacement is performed. The surgical valve replacement is performed. Direct microscopic examination and culture of the explanted and vegetative mass revealed Aspergillus section Fumiagati confirmed by molecular method. Despite the administration of voriconazole and transient improvement the patient expired. Conclusion As AE is a late consequence of COVID‐19‐associated invasive pulmonary aspergillosis, therefore, long‐term follow‐up of invasive aspergillosis, and prompt diagnosis of surgical and systemic antifungal therapy treatment, are warranted to provide robust management.