Survival rates of preterm infants have improved in the past few decades, and central venous catheters play an important role in the intensive medical treatment of these neonates. Unfortunately, these indwelling catheters increase the risk of intracardiac thrombosis, and they provide a nidus for microorganisms during the course of septicemia. Herein, we report a case of persistent bacteremia due to methicillin-resistant Staphylococcus aureus in an extremely low birth weight (ELBW) infant, along with vegetation observed on an echocardiogram, the findings which are compatible with a diagnosis of endocarditis. The endocarditis was successfully treated with antibiotic therapy, and the patient recovered without major complications. We suggest a surveillance echocardiogram for ELBW infants within a few days of birth, with regular follow-up studies when clinical signs of sepsis are observed.