Stephen L. Johnson (born March 21, 1951 in Washington D. C.) was the Administrator of the Environmental Protection Agency (EPA) under President George W. Bush during the second term of his administration.

Johnson attended Taylor University, receiving a B.A. in biology followed by a master's degree in pathology from George Washington University. Before working for the U.S. Government, he held a number of positions in laboratory and bio-technology companies. He was also the director of Hazelton Laboratories, now Covance.

Johnson began working at the EPA in 1979. He had been working at a private lab, Litton Bionetics Inc., in Washington. Johnson said that a mentor suggested he get a job at the EPA, learn about regulations from inside government, and then return to industry. "Regulations were really frustrating," Johnson told the Philadelphia Inquirer in 2008, recalling his decision to join the EPA. "I wondered if they really understood what it was like to work in a laboratory."