Upon graduation, Scott received a Rotary International Fellowship to study in Burma, where he was recruited by an American student activist who had become an anti-communist organizer for the Central Intelligence Agency (CIA). Scott agreed to do reporting for the agency, and at the end of his fellowship, took a post in the Paris office of the National Student Association, which accepted CIA money and direction in working against communist-controlled global student movements over the next few years. Scott began graduate study in political science at Yale in 1961. His dissertation on political ideology in Malaysia, which was supervised by Robert E. Lane, analyzed interviews with Malaysian civil servants. In 1967, he took a position as an assistant professor in political science at the University of Wisconsin–Madison. As a Southeast Asia specialist teaching during the Vietnam War, he offered popular courses on the war and peasant revolutions. In 1976, having earned tenure at Madison, Scott returned to Yale and settled on a farm in Durham, Connecticut with his wife. They started with a small farm, then purchased a larger one nearby in the early 1980s and began raising sheep for their wool. Since 2011, the pastures on the farm have been grazed by two Highland cattle, named Fife and Dundee.