We present a patient who developed progressive neurological disease caused by lesions histologically compatible with those observed in subacute brainstem angioencephalopathy. The patient was treated with low-molecular weight heparin, and treatment response was monitored clinically and with MRI. Anticoagulation therapy stopped progression of the neurological deficit and led to improvement of MRI findings. This report further supports the existence of subacute brainstem angioencephalopathy as a characteristic disease entity and gives insight into possible therapeutic approach with anticoagulation treatment.