In 1988, the Defense Communications Agency (DCA) absorbed the Tri-Service Tactical Communications (TRI-TAC) Joint Test Element (JTE) and the Joint Tactical Command, Control, and Communications Agency (JTC3A) Joint Interoperability Test Facility (JITF). DCA consolidated these organizations in 1989 to form the "JITC" in Fort Huachuca, Ariz. JITC's primary mission was to provide interoperability compliance testing and certification.

As the designated lead for DoD command, control, communications and intelligence (C3I) support, DCA tasked the JITC to perform interoperability tests of various systems including high frequency (HF) radio systems, Military Satellite Communications (MILSATCOM) systems, and the Worldwide Military Command and Control System (WWMCCS).

In 1992, DCA was renamed "DISA" to reflect its expanded role in managing the Defense Information Infrastructure (DII), now known as the Global Information Grid (GIG). As a result, JITC's responsibilities for ensuring joint interoperability of all military systems began to increase as well, causing the need for growth and expansion within the organization.

In 1993, the Naval Computer and Telecommunications Command (NCTC) proposed an initiative to transfer the functions and resources of the Naval Telecommunications Systems Integration Center (NAVTELSYSIC) to the JITC. Since 1976, the NAVTELSYSIC test facility operated out of Cheltenham, Maryland, and was the primary site for the Quality Assurance (QA) and Functional Certification testing of all Navy messaging systems. DISA and the Chief of Naval Operations (CNO) agreed that the transfer of NAVTELSYSIC resources to JITC would improve both agencies' ability to enhance operational fleet support. Thus, JITC's east coast arm, known as the Washington Operations Division, was established. In 1998, the Washington Operations facility was moved to the Naval Surface Warfare Center (NWSC) at Indian Head, Md.

In 2006, JITC established a test group at the DISA facility in Falls Church, Va. to support the fielding of global-net-centric solutions by providing continuous and effective T&E services to DISA joint acquisition programs within the Enterprise Services construct.

Today, testers at all JITC facilities work in concert to provide a seamless test capability in support of the armed services.