We report a rare case of a Brazilian adult woman with Ebstein’s Anomaly who presented with pacemaker endocarditis caused by Propionibacterium acnes. Ebstein’s Anomaly is a rare congenital malformation of the heart. Infective endocarditis is defined as an infection of heart valves, of the mural endocardium, of a septal defect, or of a cardiac electronic implantable device. Propionibacterium acnes is a skin commensal bacterium, that is usually considered as a contaminant, but can, on rare occasions, cause serious infections including endocarditis of prosthetic valves, native valves and cardiac electronic implantable devices. Diagnosis was made after nearly two years of investigation by identification of the organism by the MALDI-TOF technique and transoesophageal echocardiogram. The patient was successfully treated with daptomycin and device removal. She remains free of endocarditis after 32 months of follow-up.