BACKGROUND: In contrast to percutaneous atrial septal occluder device, surgical patch closure of atrial defects was known to be no infective endocarditis risk. CASE PRESENTATION: We herein report the first case of late endocarditis of surgical patch closure of atrial septal defects occurred at 47-year after surgery. On September 2014, a 56-year-old immunocompetent French Caucasian man was admitted into the Emergency Department for 3-week history of headache, acute decrease of psychomotor performance and fever at 40 °C. The diagnosis has been evoked during his admission for the management of a brain abscess and confirmed using 18F-fluorodeoxyglucose gated cardiac computed tomography (18F-FDG-PET/CT). Bacterial cultures of surgical deep samples of brain abscess were positive for Streptococcus intermedius and Aggregatibacter aphrophilus as identified by the matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF) mass spectrometry and confirmed with 16S rRNA gene sequencing. The patient was treated by antibiotics for 8 weeks and surgical patch closure removal. CONCLUSIONS: In summary, late endocarditis on surgical patch and on percutaneous atrial septal occluder device of atrial septal defects is rare. Cardiac imaging by the 18F-fluorodeoxyglucose gated cardiac computed tomography (18F-FDG-PET/CT) could improve the diagnosis and care endocarditis on surgical patch closure of atrial septal defects while transthoracic and transesophageal echocardiography remained difficult to interpret.