Bolton spent the next phase of his Air Force career in program management. In 1982, he completed correspondence courses from the Air Command and Staff College. He also attended the Defense Systems Management College of the Defense Acquisition University. From 1982 to 1985, he was posted to Wright-Patterson Air Force Base, where he was the program manager of the Lockheed Martin F-22 Raptor System Program Office. He then spent 1985–86 as a student at the Naval War College. From 1985 to 1986, he served in the Pentagon as the program element officer for the General Dynamics F-16 Fighting Falcon and as deputy division chief of the Aircraft Division, and later division chief of the Low Observables Vehicle Division in the Office of Special Programs. In 1988, Bolton returned to Wright-Patterson Air Force Base to serve as deputy program director for the Northrop Grumman B-2 Spirit Program System Office. From 1989 to 1992, he was program director of the AGM-129 ACM System Program Office at Wright-Patterson Air Force Base. Also, in 1991, he completed a master's degree in national security and strategic studies from the Naval War College. Remaining at Wright-Patterson Air Force Base, from 1992 to 1993, he was inspector general of the Air Force Materiel Command.
He was then commandant of the Defense Systems Management College at Fort Belvoir from 1993 to 1996. He spent three months as special assistant to the Assistant Secretary of the Air Force (Acquisition) in 1996, and then returned to Air Force Materiel Command as director of requirements 1996–98. From 1998 to 2000, he was Program Executive Officer for fighter and bomber programs in the Office of the Assistant Secretary of the Air Force (Acquisition). He was then commanding officer of the Air Force Security Assistance Center 2000–2002. As such, he was responsible for overseeing over $90 billion of sales of military equipment to foreign countries. He retired from the Air Force in 2002, having attained the rank of major general.
In 2002, while serving the commander of Air Force Security Assistance and Cooperation Command at Wright-Patterson AFB, President of the United StatesGeorge W. Bush asked Bolton if he would step down from that position and accept nomination as the United States Assistant Secretary of the Army for Acquisition, Logistics, and Technology. Accepting the position required Bolton to retire from the Air Force, a decision he made after discussing with his wife and daughters, and on December 31, 2001, Bolton retired at Wright Patterson. The next day, New Years Day, Bolton and his family drove to Washington D.C. and was sworn in as the United States Assistant Secretary of the Army for Acquisition, Logistics, and Technology the next day, January 2, 2002. Bolton held the office from 2 January 2002 to 2 January 2008.[5] The six years he spent in the position was at the height of the Operation Iraqi Freedom and Operation Enduring Freedom and was considered by many to be an unusually long period of time for such a stressful appointment. According to his wife, Linda Bolton, he stayed in the job for a long period because felt compelled to ensure that soldiers in battle were receiving the best equipment possible.[5]
During his tenure as the Army's senior acquisition official, Bolton received an honorary doctorate from Cranfield University in 2006, and a second honorary doctorate from his alma mater, the University of Nebraska–Lincoln, in 2007.[5]
On January 3, 2008, Bolton became executive-in-residence of the Defense Acquisition University at Fort Belvoir, where he taught DAU's executive-level Program Manager's course, a ten-week course designed for experienced acquisition practitioners who had been selected for their potential as leaders of major acquisition programs.
Bolton died unexpectedly at his home on July 28, 2015. At the time of his death he was training for the Air Force Marathon, an event he participated in annually with his two daughters.[5]
His engagement with the [Program Manager's Course] students helped to thoroughly enrich the experience for each student he interacted with, as he contributed his knowledge and experience to the course. He will be missed, not only by the students, but also by the faculty, with whom he spent many hours over the last few years, providing assistance and valuable feedback that directly influenced the quality of instruction and the course
— Dr. Michael C. Ryan, Defense Acquisition University [5]