It was no coincidence that the new field of neuroscience began to take shape in the early 1960s at MIT where cybernetics received much attention. This paper examines how the brain-computer metaphor was shared among mathematicians, computer scientists, and electrical engineers in the 1950s, and how it stimulated a biologist, Francis O. Schmitt, who laid the foundation of Neurosciences Research Program (NRP) at MIT in 1962. By analyzing his notes, speeches, and papers, made for not only scientific journals but also religious meetings, I underscore how Schmitt’s desire to develop a big theory for brain studies—something at the level of quantum theory—was reflected in the emergence of neuroscience in the U.S. I also show the effect of the decline of cybernetics in the new field of neuroscience from the mid-1970s. The ambition to unify brain studies through theory gave way to an emphasis on systematic data collection, which resulted in the launch of the U.S. Human Brain Project in the 1990s. From the vantage point of the rise and fall of the brain-computer metaphor, this paper revisits the history of neuroscience coming into its own as big science in the late twentieth century.