Theoretical neuroscience (including computational neuroscience) studies how brains process information by mathematically modeling them at the biophysical (molecular and cellular), circuit and network, and whole brain system, behavioral and social interaction levels. The Foundation supports theoretical neuroscience research that investigates basic principles and mechanisms of brain function.

The foundation supports post-doc research in theoretical neuroscience at 11 universities and scientific institutions, through centers at Harvard University (established in 2007), Princeton University, Yale University (2006), Columbia University (2005), Cold Spring Harbor Laboratory (2004), and UC San Diego (2002), and, in partnership with the Sloan Foundation, at their original five Centers for Theoretical Neurobiology (1994) at Salk Institute, Cal Tech, UC San Francisco, NYU/Courant and Brandeis University. The Swartz Foundation also sponsors conferences, workshops, seminars, and public lectures in brain science, as well as the annual Society for Neuroscience (SfN) Swartz Prize for Theoretical and Computational Neuroscience.