After the postdoctoral fellowship, Johnson was appointed assistant professor of electrical and computer engineering at the University of Colorado Boulder in 1985, where she co-founded the National Science Foundation (NSF) Engineering Research Center (ERC) for Optoelectronic Computing Systems and spun off several companies from her research laboratory including ColorLink, Inc which was later sold to RealD, responsible for the technology that helped re-launch the 3D movie industry. Additionally, she co-founded the Colorado Advanced Technology Institute Center of Excellence in Optoelectronics. In 1999, Johnson was appointed Dean of the School of Engineering at Duke University, which would be later named for distinguished alumnus, Edmund T. Pratt Jr., CEO emeritus of Pfizer Corporation.