A 77-year-old man underwent aortic valve replacement with a Carpentier-Edwards Pericardial Magna (19 mm) for aortic stenosis. He presented with a low grade fever and congestive heart failure 6 months after the initial valve replacement. Staphylococcus aureus was detected in blood culture, and peri-valvular leakage was revealed by echocardiography. Prosthetic valve endocarditis was diagnosed and underwent re-aortic valve replacement with Medtronic Mosaic 21 mm bioprothesis. Six months after the re-do operation, perivalvular leakage was newly observed between the right and non-coronary cusps, which was opposite to endocarditis affected cusps. The peri-valvular leakage was considered to have resulted from the fragile valve annulus because he did not have fever, and repeated blood culture showed no bacterial growth. We performed a third surgery and repaired the leakage by adding sutures through the right atrium and the interventricular septum to avoid directly suturing the fragile annulus. The post-operative course was uncomplicated, and no sign of endocarditis nor perivalvular leakage was observed during 9-months of observation. It is considered that the aortic valve fixation sutures through the right atrium and inter-ventricular septum are useful alternatives for fragile aortic annulus after prosthetic valve endocarditis.