William James Lynn III (born January 1, 1954) is a former United States Deputy Secretary of Defense. Before that he was Under Secretary of Defense (Comptroller) and a lobbyist for Raytheon.

Lynn was born in Key West, Florida and raised in Connecticut, graduating from New Canaan High School in June 1972. He graduated from Dartmouth College with a B.A. degree in 1976. He earned a Juris Doctor degree from Cornell Law School in 1980 and a Master of Public Affairs degree from the Woodrow Wilson School at Princeton University in 1982. Lynn was hired by the Center for Strategic and International Studies, where he served as executive director of the Defense Organization Project from 1982 to 1985. That last year, he and Barry Blechman published the book Toward a More Effective Defense. At some point, he was a senior fellow studying strategic nuclear forces and arms control at the National Defense University's Strategic Concepts Development Center, and went on to be the legislative counsel for defense and arms control matters for Massachusetts Senator Edward Kennedy between 1987 and 1993. During this time, he also worked as Kennedy's staff representative on the Committee on Armed Services.

Lynn later worked as an assistant to the Secretary of Defense for Budget, and in April 1993 joined the office of the Secretary of Defense (then Les Aspin) to be director for program analysis and evaluation. On October 21, 1997, President Bill Clinton nominated Lynn to be Under Secretary of Defense (Comptroller), and after a Senate confirmation on November 13, he was sworn in on November 19.

After leaving at the end of the Clinton Administration, Lynn became the executive vice president of the management consulting firm DFI International in 2001, but left in August 2002 when he was hired by the Raytheon Company, where he held the title senior vice president of Government Operations and Strategy.

Lynn is a member of the Atlantic Council's board of directors.

On January 8, 2009, President-elect Barack Obama nominated Lynn as his Deputy Secretary of Defense. This was complicated by the fact that new ethic rules promulgated by Obama for members of his administration created a waiting period of two years between lobbying activities and working for the administration on the same issues, which Lynn's work with Raytheon violated. President Obama waived the new rules for Lynn, which received criticism from John McCain as well as outside groups such as the Project on Government Oversight, Citizens for Responsibility and Ethics in Washington, Government Accountability Project, and Public Citizen. McCain later said that the nomination should probably move forward. As nominee, Lynn agreed to sell his holdings of Raytheon stock. Lynn's appointment was approved by the U.S. Senate Armed Services Committee on February 5, 2009, by unanimous consent. On February 11, 2009, Lynn was confirmed in the full Senate by a vote of 93–4. He took the oath of office on February 12.

In May 2009, Lynn cautioned Congress and the Obama administration about overhauling the Pentagon's weapons-buying practices. "We need to keep in mind the importance of not making the system worse in our efforts to achieve reform," he said in testimony prepared for the House Armed Services Committee. "This has happened in the past."

Lynn told lawmakers the Pentagon would hire 20,000 new people, starting in October 2009, to manage weapons acquisition, which he called "aggressive," but necessary to bring in program managers, cost estimators, software engineers and systems engineers. "We are mindful it is going to be an organizational challenge," he said.