His current work uses rational economics to develop safe and beneficial intelligent technologies for better collaborative modeling, understanding, innovation, and decision making.

Omohundro joined the International Computer Science Institute (ICSI) in Berkeley, California, where he led the development of the open source programming language Sather.

He showed that there exist smooth partial differential equations which stably perform universal computation by simulating arbitrary cellular automata.

With John David Crawford he showed that the orbits of three-dimensional period doubling systems can form an infinite number of topologically distinct torus knots and described the structure of their stable and unstable manifolds.

[22] From 1986 to 1988, he was an Assistant Professor of Computer science at the University of Illinois at Urbana-Champaign and cofounded the Center for Complex Systems Research with Stephen Wolfram and Norman Packard.