Bacterial endocarditis represents one of the most frequently acquired cardiac diseases in adult cattle. Congenital heart diseases as a ventricular septal defect can facilitate bacterial endocarditis as a consequence of turbulent blood flow through the defect, causing damage to the endocardium. We describe a case of mural endocarditis associated with a ventricular septal defect in an eight-year-old female Holstein Friesian cow. The cow’s history revealed that she had presented dysorexia and a sudden decrease of milk production in the last 10 days prior to the examination. On clinical examination, jugular pulses, tachycardia with irregular heart rate and tachypnea with harsh bronchovesicular sounds were evident. Electrocardiographic examination allowed the diagnosis of an atrial fibrillation with high ventricular response rate. Transthoracic echocardiography revealed a large vegetation originating from the endocardium between the tricuspid and pulmonic valves in the right ventricle outflow. On post-mortem examination, a small muscular septal defect under the right coronary cusp of the aortic valve and a mural vegetative endocarditis were found. An abscess in the chondro-costal junction of the third right rib and metastatic pneumonia were also observed. This case report describes a rare consequence of a small ventricular septal defect that had not been previously diagnosed in an adult cow.