Stony Brook is prominent nationally in neuroscience research. There are over 70 laboratories actively pursuing neurobiology, molecular neurobiology, behavioral neuroscience, and clinical neuroscience research.  Within the department there are research foci in the areas of multiple sclerosis, Lyme's disease, autism, epilepsy, neuro-oncology, stroke, traumatic brain injury and functional brain imaging (PET/MRI).

The Stony Brook Neurosciences Institute, directed by Dr. Dennis Choi, provides a framework to facilitate interdepartmental clinical or research programs across the university.  The SUNY Research Foundation has launched a “Brain Network of Excellence” intended to do the same for neuroscience research across the 64 SUNY campuses.  Stony Brook Neurology catalyzed discussions between the Presidents of SUNY Stony Brook and the Korea Institute for Science and Technology (KIST) in Seoul, leading to a research agreement between the two institutions focusing on translational neuroscience research.