In November 2000 Shelton moved to assume the role of Director of Requirements at the Headquarters of Air Force Space Command in Colorado Springs, Colorado.
 There he was promoted to Brigadier General on January 1, 2001.
 He stayed at Air Force Space Command until June 2003 holding various positions including Director of Plans and Programs and Director of Air and Space Operations.

Following his tour at Air Force Space Command he moved on to the United States Strategic Command on Offutt AFB in Bellevue, Nebraska.
 There he served as Director of Capability and Resource Integration and Director of Plans and Policy.
 He was also promoted to Major General on July 1, 2004.

In May 2005, Shelton moved to assume command of the 14th Air Force from Vandenberg AFB.
 In July 2006, he also assumed command of the Joint Functional Component Command for Space, which is attached to the United States Strategic Command.

The President nominated Maj Gen Shelton for the appointment to lieutenant general with continued assignment as the 14 AF/CC and CDR JFCC SPACE (Ref:  8 November 2007 Senior Leader Announcement, AF/A1).
 After Senate confirmation, Lt Gen Shelton pinned on his new rank 8 January 2008.
 Gen Kevin P. Chilton, CDRUSSTRATCOM, presided; Gen C. Robert Kehler, AFSPC/CC, also spoke during the ceremony held at Vandenberg AFB, CA.

In December 2008, Lt Gen Shelton was appointed Chief of Warfighting Integration and Chief Information Officer (CIO), Office of the Secretary of the Air Force.

On 5 January 2011, Lt General Shelton was promoted to the rank of General and became Commander, Air Force Space Command.
In November 2000 Shelton moved to assume the role of Director of Requirements at the Headquarters of Air Force Space Command in Colorado Springs, Colorado.  There he was promoted to Brigadier General on January 1, 2001.  He stayed at Air Force Space Command until June 2003 holding various positions including Director of Plans and Programs and Director of Air and Space Operations.
Following his tour at Air Force Space Command he moved on to the United States Strategic Command on Offutt AFB in Bellevue, Nebraska.  There he served as Director of Capability and Resource Integration and Director of Plans and Policy.  He was also promoted to Major General on July 1, 2004.
In May 2005, Shelton moved to assume command of the 14th Air Force from Vandenberg AFB.  In July 2006, he also assumed command of the Joint Functional Component Command for Space, which is attached to the United States Strategic Command.
The President nominated Maj Gen Shelton for the appointment to lieutenant general with continued assignment as the 14 AF/CC and CDR JFCC SPACE (Ref:  8 November 2007 Senior Leader Announcement, AF/A1).  After Senate confirmation, Lt Gen Shelton pinned on his new rank 8 January 2008.  Gen Kevin P. Chilton, CDRUSSTRATCOM, presided; Gen C. Robert Kehler, AFSPC/CC, also spoke during the ceremony held at Vandenberg AFB, CA.
In December 2008, Lt Gen Shelton was appointed Chief of Warfighting Integration and Chief Information Officer (CIO), Office of the Secretary of the Air Force.
On 5 January 2011, Lt General Shelton was promoted to the rank of General and became Commander, Air Force Space Command.
William L. Shelton