A 73-year-old man underwent aortic valve replacement (AVR) with a bioprosthetic valve for severe aortic regurgitation at another hospital 18 months ago. He was referred to our department for treatment due to thickening of the bioprosthetic valve leaflets and restricted valve motion. Additionally, a 13×13 mm abnormal structure, suspected to be vegetation, was observed at the left ventricular outflow tract (LVOT). Because this tissue could cause an embolism and the patient exhibited severe aortic stenosis due to constriction of the valve orifice area by the vegetation, the heart team decided that redo AVR was necessary. The patient underwent redo surgery via a re-median sternotomy. A fragile vegetation, characterized by a pale pink and black mixture, was adherent to the prosthetic valve leaflet and its inner surface. Upon removal of the prosthetic valve, the same type of tissue was observed at the LVOT under the right coronary cusp. The aortic valve was replaced with a sutureless bioprosthetic valve. The excised vegetation was culture-negative, as was the prosthetic valve. Histological examination revealed that the vegetation primarily consisted of fibrin, with small amounts of erythrocytes and histiocyte inclusions. Based on the tissue's origin and histological findings, we diagnosed nonbacterial thrombotic endocarditis (NBTE) as the cause of the early prosthetic valve dysfunction. NBTE should be considered one of the differential diagnoses for early prosthetic valve dysfunction.