After finishing his doctorate in 1981, Farmer took a post-doctoral appointment at the Center for Nonlinear Studies at Los Alamos National Laboratory and received an Oppenheimer Fellowship in 1983. He developed an interest in what is now called complex systems and co-organized several seminal conferences in this area. In 1988 he founded the Complex Systems Group in the Theoretical Division and recruited a group of postdoctoral fellows who subsequently became leaders in the field, including Kunihiko Kaneko, Chris Langton, Walter Fontana, Steen Rasmussen, David Wolpert, Stephanie Forrest, James Theiler and Seth Lloyd.