Gilligan's departure coincides with an Air Force reorganization that combines his office with warfighting integration and communications operations into a single directorate.
Recently, Gilligan worked with Microsoft to consolidate the Air Force's multiple software and services contracts into two enterprise agreements. In an interview in December, Gilligan said the deal would produce standard configurations that would enforce strict security policies for all Microsoft desktop and server software used by Air Force personnel, and streamline patching.
Gilligan became the Air Force's CIO in 2001, after serving two years as the Deparment of Energy's CIO. He previously worked as the principal deputy assistant secretary of the Air Force for business and information management and as deputy CIO.
"John has led extraordinary efforts to adapt Air Force information technology capabilities for future challenges," Michael Dominguez, acting secretary of the Air Force, said in a statement. "His initiatives will benefit all Airmen and our contributions to the joint warfighting team for years to come."
Gilligan has not finalized his plans for transitioning to the private sector, according to the Air Force.
The new directorate will centralize IT policy formulation, execution, resources, and workforce governance. Air Force officials have said a three-star general will head it.