Background Intramedullary spinal cord abscesses (ISCA) are rare, even more so in association with brain abscesses. Infective endocarditis is an uncommon cause of ISCA. In this case study, we report a patient with intramedullary abscesses and multiple brain abscesses due to subacute infective endocarditis. Case presentation A 54-year-old man presented with a 7-day history of head and neck pain and numbness in both lower limbs. Intramedullary abscess combined with multiple brain abscesses was diagnosed based on blood culture, head and spinal magnetic resonance imaging (MRI), contrast-enhanced MRI, and magnetic resonance spectroscopy. Echocardiography revealed vegetations on the mitral valve and severe mitral regurgitation, which the authors believe was caused by subacute infective endocarditis. With ceftriaxone combined with linezolid anti-infective therapy, the patient's symptoms and imaging was improved during follow-up. Conclusions This case hopes to raise the vigilance of clinicians for ISCA. When considering a patient with an ISCA, it is necessary to complete blood culture, MRI of the brain and spinal cord, and echocardiography to further identify whether the patient also has a brain abscess and whether the cause is infective endocarditis.