We report a case of infective endocarditis after flexible sigmoidoscopy. In addition to persistent bacteremia with methicillin-resistant Staphylococcus aureus (MRSA), we found an oscillating intracardiac mass on the tricuspid valve in this patient. The patient had no underlying heart disease or risk factor for the infection due to MRSA. Vancomycin treatment for 42 days was adequate for this case. The pathogen might colonize the patient's rectum and then invade through intestinal mucosa during the endoscopic procedure.