Rubber band ligation is a common option used to treat symptomatic internal hemorrhoids. Severe complications such as pelvic sepsis are a rare occurrence. We report a case of endocarditis leading to septic pulmonary and renal emboli following single-quadrant rubber band ligation. The patient had a known ventricular septal defect and developed low back pain and fever after ligation of a right anterior internal hemorrhoid. He was found to have septic pulmonary emboli, a renal wedge septic infarct, and a large vegetation on his membranous ventricular septal defect requiring operative intervention. Before this report, rubber band ligation has not been associated with endocarditis. According to several guidelines, this patient did not require antibiotic prophylaxis. It is unclear whether prophylaxis could have prevented this complication. Surgeons utilizing rubber band ligation need to be familiar with all potential complications.