ENJJPT’s organization is as unique as its mission. Overall responsibility for the program lies not within its structure, but rather with all the member nations. Each nation has a representative on the "Steering Committee." This is a separate governing body tasked with the formation of policy and oversight of the program as a whole. The Steering Committee has direct access to each member nation’s Air Staff or Headquarters and is empowered by the two founding documents of ENJJPT; the Memorandum of Understanding and the Plan of Operation. 

Command of ENJJPT is given to the commander of the United States Air Education and Training Command and is delegated to the 19th Air Force commander. Locally, the 80th Flying Training Wing (FTW) wing commander oversees day-to-day operations and implementation of training policies. 

Because of the United States’ status as the host nation, the Wing Commander of the 80 FTW is always a US officer. The European nation having the largest number of students fills the position of Operations Group Commander (OG/CC). The Deputy Operations Group Commander (OG/CD) is a US officer. 

The 80th Flying Training Wing is composed of the Operations Group and 4 Wing Staff Agencies: Resource Management, the Quality Office, Wing Safety, and Maintenance Management. The Operations Group consists of four squadrons: the 80th Operations Support Squadron, the 88th Flying Training Squadron, the 89th Flying Training Squadron, and the 90th Flying Training Squadron. 

The 80 OSS is a support organization for all flying operations at ENJJPT. Some of its responsibilities include airfield and airspace management, weather services, air traffic control, flight records, programming, life support, computer systems, and information management for all students and permanent party personnel. The 80 OSS also coordinates with the 82 Training Wing, Sheppard’s host unit, on various support functions relating to ENJJPT. 

The 88 FTS is home to the "Introduction to Fighter Fundamentals" program which is the lead in training school for pilot graduates going on to fighter weapons systems and the Pilot Instructor Training (PIT) program which trains instructors for the ENJJPT program. The 89th and 90th are tasked with T-37 and T-38 training, respectively. Command of these squadrons rotates among officers from each member nation. 

Instructor pilot manning within each squadron is determined by student participation. Each nation provides instructor pilots proportionate to the number of students in attendance.