From 1974 to 1984, Scott served as a research biologist for the U.S. Fish and Wildlife Service at Mauna Loa Field Station in Hawaii Volcanoes National Park. It was his first assignment with the U.S. Department of Interior. From 1984 to 1986, he served as project leader of the California Condor Research Center in Ventura. In 1986 he was appointed to his current position as leader of the Idaho Cooperative Fish and Wildlife Research Unit in Moscow, Idaho. In addition, he is a professor in the Department of Fish and Wildlife Resources at the University of Idaho, where he pioneered the Gap Analysis Program and served as program leader from 1989 to 1997.