William Thomas entered the U.S. Air Force Academy on June 28, 1982, and was commissioned a 2d Lt on May 28, 1986. Lt Thomas next completed Undergraduate Pilot Training and was awarded his pilot wings at Laughlin AFB, Texas, in November 1987, followed by F-16 Fighting Falcon training from November 1987 to July 1988. He served as an F-16 pilot and instructor pilot with the 14th Fighter Squadron at Misawa AB, Japan, from July 1988 to July 1991, and then served as a Project Officer with the 4484th Test Squadron at Tyndall AFB, Florida, from July 1991 to June 1992. Capt Thomas attended F-16 Fighter Weapons School at Nellis AFB, Nevada, from June to December 1992, and then served as a Radar Project Officer and F-16 Operational Test Pilot with the 84th Test Squadron at Tyndall AFB from January 1993 to March 1994. His next assignment was as an F-16 pilot and Chief of Weapons and Tactics with the 35th Fighter Squadron at Kunsan AB, South Korea, from March 1994 to March 1995, followed by service as an F-16 pilot and Chief of Weapons and Tactics with the 14th Fighter Squadron and as Weapons Officer for the 35th Fighter Wing at Misawa AB from March 1995 to April 1998. Maj Thomas attended Dutch Language School at the International Center for Language Studies in Washington, D.C., from April to October 1988, and then served as an Instructor Pilot and Operations Officer with the NATO Fighter Weapons School at Leeuwarden AB, The Netherlands, from October 1998 to June 2001, during which time he participated in combat missions in Kosovo. Lt Col Thomas next served as Chief of Weapons and Tactics, as an Operations Officer, and then as Chief of Advanced Programs with the 52nd Fighter Wing at Spangdahlem AB, Germany, from June 2001 to October 2003, followed by service as an Operations Officer on the Joint Staff in the Pentagon from October 2003 to August 2004. He attended the Industrial College of the Armed Forces at Fort McNair, Washington, D.C., from August 2004 to June 2005, and then served as Deputy Chief of the Operations Division on the Joint Staff at the Pentagon from June 2005 to June 2007. Col Thomas next served as the Director of Operations for U.S. Central Command Air Forces at the Combined Air and Space Operations Center in Qatar from June 2007 to June 2008, followed by service as Commander of the 4th Mission Support Group at Seymour Johnson AFB, North Carolina, from June 2008 to July 2010. His final assignment was as Chief of the Weapons Division at Headquarters U.S. Air Force in the Pentagon from July 2010 until his retirement from the Air Force on August 1, 2012.

His Silver Star Citation reads:

Major William L. Thomas, Jr., distinguished himself by gallantry in connection with military operations against an opposing armed force over Kosovo, the Former Republic of Yugoslavia, in support of Operation ALLIED FORCE, on 7 June 1999. On that date, despite being fired upon by two SA-3 surface-to-air missiles and continuous AAA fire, Major Thomas located a total of four MIG-29 aircraft, destroyed two, his wingman destroyed one and he handed off the last to a flight of F-15Es. During the second attack run on the airfield, a heavily defended Batajnica airfield, Northwest of Belgrade, Major Thomas' wingman was forced to execute several defensive reactions to surface-to-air missiles, the second missile plume momentarily blinded his wingman, resulting in his wingman doing a low altitude dive recovery in the heart of the AAA. Major Thomas directed his wingman to egress, regain energy and climb. With complete disregard for his personal safety, Major Thomas flew over the AAA dispensing flares, causing the AAA to target him instead of his wingman. This maneuver distracted the AAA long enough for his wingman to safely egress the target area. By his gallantry and devotion to duty, Major Thomas has reflected great credit upon himself and the United States Air Force.