The Department of Cognitive Science began as the Cognitive Science Center in July 1987. Studies in cognitive science were already being done in other departments, including psychology, philosophy, biophysics, and computer science. In March 1985, Alfonso Caramazza, Professor of Psychology, and Shin Lin, Professor of Biophysics, recommended to the president that an institute be created for the study of the brain and cognition. They proposed to build two centers, one for neuroscience and one for cognitive science, which would be integrated at a later time.

The center for neuroscience became the Mind/Brain Institute, for which the Homewood Committee made a proposal in December 1985. The committee wrote that the Mind/Brain Institute would "facilitate the synthesis and integration" of studies of mind and brain which were already being done in other disciplines, and foster more interdisciplinary research and training programs. The Mind/Brain Institute would employ neuroscientists, who study the physical parts of the body, the nervous system, its cellular and molecular properties, and electrical and chemical mechanisms of neurons.

In contrast with neuroscience, cognitive scientists study the structure and content of intelligent processes independent of the physical parts of the body in which they take place. The Cognitive Science Center was formed to study how organisms (especially humans) represent, use, manipulate, and acquire information. In their January 1987 proposal for the Cognitive Science Center, Alfonso Caramazza, David Olton, Joseph O'Rourke, Terrence Sejnowski, and George Wilson recommended that the Center's faculty be drawn from among members of current departments at Homewood and at the School of Medicine: Psychology, Neurology, Philosophy, Biophysics, and Neuroscience. The Center would also promote a new discipline, Artificial Intelligence. The Center began offering courses leading to the BA and PhD in 1990, and in the same year became the Department of Cognitive Science. The faculty of the department are currently:

Alfonso Caramazza, Professor and Director
Stephen R. Anderson, Professor
Michael E. McCloskey, Professor
Luigi Burzio, Visiting Associate Professor
William Badecker, Associate Research Scientist and Assistant Professor
Howard Egeth, Professor (joint appt. with Psychology)
Simon Kasif, Assistant Professor (joint appt. with Computer Science)
Guy McKhann (joint appt. with Neurology, Neuroscience, and Director of Mind/Brain Institute)
Steven Salzberg, Assistant Professor (joint appt. with Computer Science)
George Wilson, Professor (joint appt. with Philosophy)
Steven Yantis, Assistant Professor (joint appt. with Psychology)