A 52-year-old woman developed congestive heart failure and was diagnosed with aortic regurgitation with approximately 20 mm of vegetation located on the noncoronary cusp of the aortic valve. The patient had undergone tooth extraction 3 months earlier, and various antibiotics had been given in the treatment of refractory high fever for 1 month. The damage to the aortic valve extended to the fibrous trigone near the mitral valve, and aggressive debridement of necrotic and infected tissue was done. The excised defect was repaired and reinforced with a pericardial patch, and the Freestyle stentless bioprosthesis was implanted using the full-root technique. Although the causative organism was never isolated, recurrent endocarditis has not occurred during 3 years of follow-up. The Freestyle stentless bioprosthesis was useful in the management of active aortic infectious endocarditis with undetermined causative organism for the prevention of recurrent endocarditis in the early postoperative period.